ClinVar Genomic variation as it relates to human health
NM_000059.4(BRCA2):c.6656C>G (p.Ser2219Ter)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000059.4(BRCA2):c.6656C>G (p.Ser2219Ter)
Variation ID: 52149 Accession: VCV000052149.26
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 13q13.1 13: 32341011 (GRCh38) [ NCBI UCSC ] 13: 32915148 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 1, 2014 May 1, 2024 Sep 8, 2016 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000059.4:c.6656C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000050.3:p.Ser2219Ter nonsense NC_000013.11:g.32341011C>G NC_000013.10:g.32915148C>G NG_012772.3:g.30532C>G LRG_293:g.30532C>G LRG_293t1:c.6656C>G LRG_293p1:p.Ser2219Ter U43746.1:n.6884C>G - Protein change
- S2219*
- Other names
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- Canonical SPDI
- NC_000013.11:32341010:C:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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BRCA2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
18938 | 19097 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (6) |
reviewed by expert panel
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Sep 8, 2016 | RCV000113622.16 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jun 29, 2022 | RCV000447889.15 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Nov 10, 2023 | RCV000502225.17 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 31, 2018 | RCV000763324.10 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 8, 2023 | RCV000985568.11 | |
Pathogenic (1) |
no assertion criteria provided
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- | RCV001353656.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 5, 2022 | RCV001813752.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Apr 25, 2022 | RCV003473386.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Sep 08, 2016)
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reviewed by expert panel
Method: curation
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Breast-ovarian cancer, familial, susceptibility to, 2
Affected status: unknown
Allele origin:
germline
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Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Accession: SCV000301087.2
First in ClinVar: Sep 24, 2016 Last updated: Sep 24, 2016 |
Comment:
Variant allele predicted to encode a truncated non-functional protein.
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Pathogenic
(Apr 24, 2018)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 2
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000786396.2
First in ClinVar: Nov 05, 2016 Last updated: Nov 05, 2016 |
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Pathogenic
(Oct 31, 2018)
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criteria provided, single submitter
Method: clinical testing
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Familial cancer of breast
Medulloblastoma Familial prostate cancer Wilms tumor 1 Fanconi anemia complementation group D1 Breast-ovarian cancer, familial, susceptibility to, 2 Glioma susceptibility 3 Pancreatic cancer, susceptibility to, 2
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000894001.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
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Pathogenic
(Oct 02, 2015)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 2
Affected status: unknown
Allele origin:
germline
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Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge
Accession: SCV000327487.4
First in ClinVar: Nov 05, 2016 Last updated: Dec 11, 2022 |
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Pathogenic
(Jul 02, 2018)
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criteria provided, single submitter
Method: clinical testing
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Hereditary breast and ovarian cancer syndrome
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV000838844.2
First in ClinVar: Oct 10, 2018 Last updated: Dec 11, 2022 |
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Pathogenic
(Mar 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV003840660.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of … (more)
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 6884C>G; This variant is associated with the following publications: (PMID: 28918466, 20104584, 27425403, 32885271, 33754277, 25525159, 27553368, 12655567, 29348823, 26026974, 16389418, 16168123, 16758124, 29907814, 29161300, 30606148, 29446198, 35264596, 9150174, 19967274, 17063270, 21120943, 21520273, 24312913, 31209999, 32377563) (less)
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Pathogenic
(Apr 25, 2022)
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criteria provided, single submitter
Method: clinical testing
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Familial cancer of breast
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004212810.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Feb 21, 2019)
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criteria provided, single submitter
Method: clinical testing
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Hereditary breast and ovarian cancer syndrome
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001360637.1
First in ClinVar: Jun 22, 2020 Last updated: Jun 22, 2020 |
Comment:
Variant summary: BRCA2 c.6656C>G (p.Ser2219X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Variant summary: BRCA2 c.6656C>G (p.Ser2219X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. c.6757_6758delCT/p.Leu2253fsX7, c.6761_6762delTT/p.Phe2254fsX6). The variant was absent in 245654 control chromosomes. c.6656C>G has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer (Dufloth_2005, Caux-Moncoutier_2011, Borg_2010, Alemar_2016, Pinto_2016). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Jun 18, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001133869.3
First in ClinVar: Jan 06, 2020 Last updated: Jan 03, 2022 |
Comment:
The variant creates a premature nonsense codon, and is therefore predicted to result in the loss of a functional protein. Found in at least one … (more)
The variant creates a premature nonsense codon, and is therefore predicted to result in the loss of a functional protein. Found in at least one symptomatic patient, and not found in general population data. (less)
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Pathogenic
(Jan 15, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV000537687.3
First in ClinVar: Mar 25, 2017 Last updated: Jan 15, 2022 |
Comment:
This variant changes 1 nucleotide in exon 11 of the BRCA2 gene, creating a premature translation stop signal. This variant is expected to result in … (more)
This variant changes 1 nucleotide in exon 11 of the BRCA2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. (less)
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Pathogenic
(Jan 05, 2022)
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criteria provided, single submitter
Method: clinical testing
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BRCA2-related disorder
Affected status: yes
Allele origin:
germline
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DASA
Accession: SCV002061199.1
First in ClinVar: Jan 22, 2022 Last updated: Jan 22, 2022 |
Comment:
The c.6656C>G;p.(Ser2219*) variant creates a premature translational stop signal in the BRCA2 gene. It is expected to result in an absent or disrupted protein product … (more)
The c.6656C>G;p.(Ser2219*) variant creates a premature translational stop signal in the BRCA2 gene. It is expected to result in an absent or disrupted protein product -PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 52149; PMID: 16168123; 12655567; 29907814; 31209999; 30606148; 19967274; 16389418; 29348823; 29446198; 27425403; 26026974; 24312913; 17063270; 9150174; 28918466; 27553368) - PS4. This variant is not present in population databases (rs80358893, gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. In summary, the currently available evidence indicates that the variant is pathogenic. (less)
Number of individuals with the variant: 1
Sex: female
Geographic origin: Brazil
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Pathogenic
(Dec 13, 2021)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 2
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002579685.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022
Comment:
ACMG criteria applied: PVS1, PS4, PM2_SUP, PP4
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Number of individuals with the variant: 1
Sex: female
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Pathogenic
(Nov 10, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary breast ovarian cancer syndrome
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001591496.4
First in ClinVar: May 10, 2021 Last updated: Feb 28, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Ser2219*) in the BRCA2 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Ser2219*) in the BRCA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with breast cancer (PMID: 12655567, 16389418, 20104584). ClinVar contains an entry for this variant (Variation ID: 52149). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Nov 13, 2023)
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criteria provided, single submitter
Method: clinical testing
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Breast-ovarian cancer, familial, susceptibility to, 2
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004844292.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
The c.6656C>G (p.Ser2219*) variant in the BRCA2 gene is located on the exon 11 and introduces a premature translation termination codon (p.Ser2219*), resulting in an … (more)
The c.6656C>G (p.Ser2219*) variant in the BRCA2 gene is located on the exon 11 and introduces a premature translation termination codon (p.Ser2219*), resulting in an absent or disrupted protein product. The variant has been reported in multiple individuals with breast and/or ovarian cancer (PMID: 36119527, 30606148, 27425403, 27553368). Loss-of-function variants of BRCA2 are known to be pathogenic (PMID: 8988179, 11897832, 29446198). The variant is reported in ClinVar as pathogenic (ID: 52149) and reviewed by the expert panel. The variant is absent in the general population database (gnomAD). Therefore, the c.6656C>G (p.Ser2219*) variant of BRCA2 has been classified as pathogenic. (less)
Number of individuals with the variant: 1
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Pathogenic
(Jun 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000661160.5
First in ClinVar: Mar 25, 2017 Last updated: May 01, 2024 |
Comment:
The p.S2219* pathogenic mutation (also known as c.6656C>G), located in coding exon 10 of the BRCA2 gene, results from a C to G substitution at … (more)
The p.S2219* pathogenic mutation (also known as c.6656C>G), located in coding exon 10 of the BRCA2 gene, results from a C to G substitution at nucleotide position 6656. This changes the amino acid from a serine to a stop codon within coding exon 10. This mutation has been identified in multiple individuals and families with hereditary breast and ovarian cancer syndrome (Ramus SJ et al. Am. J. Hum. Genet. 1997 May;60:1242-6; Duran M et al. Hum. Mutat. 2003 Apr;21:448; Borg A et al. Hum. Mutat. 2010 Mar;31:E1200-40; Alemar B et al. Cancer Genet. 2016 Sep;209:417-422; Pinto P et al. Breast Cancer Res. Treat. 2016 Sep;159:245-56; Hirasawa A et al. Oncotarget. 2017 Nov 28;8(68):112258-112267). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(May 29, 2002)
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no assertion criteria provided
Method: clinical testing
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Breast-ovarian cancer, familial 2
Affected status: yes
Allele origin:
germline,
unknown
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Breast Cancer Information Core (BIC) (BRCA2)
Accession: SCV000146903.2
First in ClinVar: Apr 01, 2014 Last updated: Apr 01, 2014 |
Observation 1:
Number of individuals with the variant: 1
Observation 2:
Number of individuals with the variant: 1
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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Malignant tumor of breast
Affected status: yes
Allele origin:
unknown
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Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000592068.2 First in ClinVar: Aug 28, 2017 Last updated: Apr 13, 2021 |
Comment:
The BRCA2 p.Ser2219* variant was identified in 7 of 3898 proband chromosomes (frequency: 0.002) from individuals or families with breast or ovarian cancer (Alemar 2016, … (more)
The BRCA2 p.Ser2219* variant was identified in 7 of 3898 proband chromosomes (frequency: 0.002) from individuals or families with breast or ovarian cancer (Alemar 2016, Borg 2010, Dufloth 2005, Palmero 2018, Pinto 2016). The variant was also identified in dbSNP (ID: rs80358893) as "With Pathogenic allele", ClinVar (classified as pathogenic by Ambry Genetics, Color, Counsyl, and five other submitters), LOVD 3.0 (1x as pathogenic), and UMD-LSDB (8x as causal). The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The p.Ser2219* variant leads to a premature stop codon at position 2219, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the BRCA2 gene are an established mechanism of disease in hereditary breast and ovarian cancer and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. (less)
Number of individuals with the variant: 2
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Characterization of genetic predisposition to molecular subtypes of breast cancer in Brazilian patients. | Paixão D | Frontiers in oncology | 2022 | PMID: 36119527 |
The spectrum of BRCA1 and BRCA2 pathogenic sequence variants in Middle Eastern, North African, and South European countries. | Laitman Y | Human mutation | 2019 | PMID: 31209999 |
Prevalence of BRCA1 and BRCA2 pathogenic and likely pathogenic variants in non-selected ovarian carcinoma patients in Brazil. | Cotrim DP | BMC cancer | 2019 | PMID: 30606148 |
The germline mutational landscape of BRCA1 and BRCA2 in Brazil. | Palmero EI | Scientific reports | 2018 | PMID: 29907814 |
Mutational spectrum in a worldwide study of 29,700 families with BRCA1 or BRCA2 mutations. | Rebbeck TR | Human mutation | 2018 | PMID: 29446198 |
Mutations in context: implications of BRCA testing in diverse populations. | Felix GES | Familial cancer | 2018 | PMID: 28918466 |
Prevalence of pathogenic germline variants detected by multigene sequencing in unselected Japanese patients with ovarian cancer. | Hirasawa A | Oncotarget | 2017 | PMID: 29348823 |
Implementation of next-generation sequencing for molecular diagnosis of hereditary breast and ovarian cancer highlights its genetic heterogeneity. | Pinto P | Breast cancer research and treatment | 2016 | PMID: 27553368 |
Prevalence of Hispanic BRCA1 and BRCA2 mutations among hereditary breast and ovarian cancer patients from Brazil reveals differences among Latin American populations. | Alemar B | Cancer genetics | 2016 | PMID: 27425403 |
BRCA1 and BRCA2 mutations in males with familial breast and ovarian cancer syndrome. Results of a Spanish multicenter study. | de Juan I | Familial cancer | 2015 | PMID: 26026974 |
A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer. | Karami F | BioMed research international | 2013 | PMID: 24312913 |
Assessment of rare BRCA1 and BRCA2 variants of unknown significance using hierarchical modeling. | Capanu M | Genetic epidemiology | 2011 | PMID: 21520273 |
EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. | Caux-Moncoutier V | Human mutation | 2011 | PMID: 21120943 |
Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. | Borg A | Human mutation | 2010 | PMID: 20104584 |
Screening for BRCA1 and BRCA2 mutations in breast cancer patients from Mexico: the public health perspective. | Narod SA | Salud publica de Mexico | 2009 | PMID: 19967274 |
Prevalence of BRCA1 and BRCA2 mutations in breast cancer patients from Brazil. | Gomes MC | Breast cancer research and treatment | 2007 | PMID: 17063270 |
High proportion of novel mutations of BRCA1 and BRCA2 in breast/ovarian cancer patients from Castilla-León (central Spain). | Infante M | Journal of human genetics | 2006 | PMID: 16758124 |
Analysis of BRCA1 and BRCA2 mutations in Brazilian breast cancer patients with positive family history. | Dufloth RM | Sao Paulo medical journal = Revista paulista de medicina | 2005 | PMID: 16389418 |
Strong evidence that the common variant S384F in BRCA2 has no pathogenic relevance in hereditary breast cancer. | Wappenschmidt B | Breast cancer research : BCR | 2005 | PMID: 16168123 |
Mutational analysis of BRCA2 in Spanish breast cancer patients from Castilla-Leon: identification of four novel truncating mutations. | Duran M | Human mutation | 2003 | PMID: 12655567 |
Contribution of BRCA2 germline mutations to hereditary breast/ovarian cancer in Germany. | Hamann U | Journal of medical genetics | 2002 | PMID: 11897832 |
Analysis of BRCA1 and BRCA2 mutations in Hungarian families with breast or breast-ovarian cancer. | Ramus SJ | American journal of human genetics | 1997 | PMID: 9150174 |
Variation of risks of breast and ovarian cancer associated with different germline mutations of the BRCA2 gene. | Gayther SA | Nature genetics | 1997 | PMID: 8988179 |
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Text-mined citations for rs80358893 ...
HelpRecord last updated Sep 17, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.