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NM_000535.7(PMS2):c.1557T>C (p.Tyr519=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Mar 31, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000141664.8
Variation ID:
141664
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.1557T>C (p.Tyr519=)

Allele ID
151378
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5987208 (GRCh38) GRCh38 UCSC
7: 6026839 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.6026839A>G
NC_000007.14:g.5987208A>G
NM_000535.7:c.1557T>C MANE Select NP_000526.2:p.Tyr519= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:5987207:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00978 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.01065
1000 Genomes Project 0.00978
The Genome Aggregation Database (gnomAD), exomes 0.00237
The Genome Aggregation Database (gnomAD) 0.00988
Exome Aggregation Consortium (ExAC) 0.00306
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01023
Links
ClinGen: CA009853
dbSNP: rs6972869
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Apr 22, 2015 RCV000130271.3
Benign 2 criteria provided, multiple submitters, no conflicts Feb 2, 2017 RCV000174013.1
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000205619.6
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV000524438.5
Benign 1 no assertion criteria provided - RCV001357173.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PMS2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3057 3122

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 22, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686138.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Feb 02, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000806178.1
Submitted: (Jan 29, 2018)
Evidence details
Benign
(Aug 06, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225237.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal cancer type 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000469728.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Nov 18, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000185116.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Seen in trans with a mutation or in homozygous state in individual without severe disease for that gene
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000262045.8
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Oct 26, 2017)
no assertion criteria provided
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
True Health Diagnostics
Accession: SCV000788105.1
Submitted: (Mar 08, 2018)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001552547.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The PMS2 p.Tyr519= variant was identified in 1 of 792 proband chromosomes (frequency: 0.001) from Dutch individuals or families with MMR-deficient cancer, or positive family … (more)

Functional evidence

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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.

Text-mined citations for rs6972869...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021