ClinVar Genomic variation as it relates to human health
NM_004629.2(FANCG):c.1077-2A>G
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_004629.2(FANCG):c.1077-2A>G
Variation ID: 445394 Accession: VCV000445394.21
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 9p13.3 9: 35076030 (GRCh38) [ NCBI UCSC ] 9: 35076027 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Nov 5, 2017 Jun 17, 2024 Jan 21, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_004629.2:c.1077-2A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
splice acceptor NC_000009.12:g.35076030T>C NC_000009.11:g.35076027T>C NG_007312.1:g.8987A>G NG_007887.1:g.1713A>G LRG_499:g.8987A>G LRG_499t1:c.1077-2A>G LRG_657:g.1713A>G - Protein change
- Other names
- -
- Canonical SPDI
- NC_000009.12:35076029:T:C
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
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.
-
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00001
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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. |
|||
FANCG | - | - |
GRCh38 GRCh37 |
924 | 1006 |
Conditions - Germline
Condition
Help
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
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Mar 26, 2022 | RCV000514018.14 | |
Pathogenic (1) |
criteria provided, single submitter
|
Dec 22, 2023 | RCV000695845.13 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
|
Jan 21, 2024 | RCV000760153.15 |
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. |
|
---|---|---|---|---|---|
Pathogenic
(May 31, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: not provided
Allele origin:
germline
|
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000609726.1
First in ClinVar: Nov 05, 2017 Last updated: Nov 05, 2017 |
|
|
Pathogenic
(Mar 31, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group G
Affected status: yes
Allele origin:
germline
|
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota
Accession: SCV000889968.1
First in ClinVar: Mar 19, 2019 Last updated: Mar 19, 2019 |
Number of individuals with the variant: 1
|
|
Pathogenic
(Feb 09, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV002051563.2
First in ClinVar: Jan 08, 2022 Last updated: Feb 11, 2022 |
Comment:
PVS1, PS3, PM2
|
|
Pathogenic
(Nov 27, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group G
Affected status: yes
Allele origin:
germline
|
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Accession: SCV002512455.1
First in ClinVar: May 21, 2022 Last updated: May 21, 2022 |
Comment:
ACMG classification criteria: PVS1 very strong, PS3 supporting, PS4 moderate, PM2 moderate, PM3 moderate, PP1 supporting
Geographic origin: Brazil
|
|
Pathogenic
(Mar 26, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV002578528.2
First in ClinVar: Oct 15, 2022 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate a damaging effect (exon skipping or usage of a cryptic splice donor site leading to multiple aberrant transcripts) (Auerbach et al., … (more)
Published functional studies demonstrate a damaging effect (exon skipping or usage of a cryptic splice donor site leading to multiple aberrant transcripts) (Auerbach et al., 2003); This variant is associated with the following publications: (PMID: 25525159, 11438206, 33718801, 11093276, 12552564) (less)
|
|
Pathogenic
(Dec 22, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV000824367.6
First in ClinVar: Oct 10, 2018 Last updated: Feb 20, 2024 |
Comment:
This sequence change affects an acceptor splice site in intron 8 of the FANCG gene. RNA analysis indicates that disruption of this splice site induces … (more)
This sequence change affects an acceptor splice site in intron 8 of the FANCG gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs769547477, gnomAD 0.009%). Disruption of this splice site has been observed in individuals with Fanconi anaemia (PMID: 11093276, 12552564, 28717661). This variant is also known as IVS8-2A>G. ClinVar contains an entry for this variant (Variation ID: 445394). Studies have shown that disruption of this splice site results in skipping of exon 9 and activation of a cryptic splice site and introduces a premature termination codon (PMID: 11093276). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(May 26, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group G
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV002791021.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
|
|
Pathogenic
(Jan 21, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group G
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV004199169.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
|
|
Pathogenic
(Feb 28, 2020)
|
no assertion criteria provided
Method: curation
|
Fanconi anemia complementation group G
Affected status: no
Allele origin:
germline
|
Leiden Open Variation Database
Accession: SCV001364827.1
First in ClinVar: Jun 29, 2020 Last updated: Jun 29, 2020 |
Comment:
Curator: Arleen D. Auerbach. Submitters to LOVD: Arleen D. Auerbach, Avani P. Solanki, Daniela Pilonetto, Johan de Winter.
|
|
Pathogenic
(Sep 16, 2020)
|
no assertion criteria provided
Method: clinical testing
|
Fanconi anemia group G
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV001452302.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
|
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 |
---|---|---|---|---|
A strategy for molecular diagnostics of Fanconi anemia in Brazilian patients. | Pilonetto DV | Molecular genetics & genomic medicine | 2017 | PMID: 28717661 |
Genetic subtyping of Fanconi anemia by comprehensive mutation screening. | Ameziane N | Human mutation | 2008 | PMID: 17924555 |
Spectrum of sequence variation in the FANCG gene: an International Fanconi Anemia Registry (IFAR) study. | Auerbach AD | Human mutation | 2003 | PMID: 12552564 |
Functional analysis of patient-derived mutations in the Fanconi anemia gene, FANCG/XRCC9. | Nakanishi K | Experimental hematology | 2001 | PMID: 11438206 |
Spectrum of mutations in the Fanconi anaemia group G gene, FANCG/XRCC9. | Demuth I | European journal of human genetics : EJHG | 2000 | PMID: 11093276 |
Text-mined citations for rs769547477 ...
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.