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NM_000535.7(PMS2):c.251-20T>G

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 2, 2021)
Last evaluated:
Jul 14, 2020
Accession:
VCV000127785.9
Variation ID:
127785
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.251-20T>G

Allele ID
133242
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 6003812 (GRCh38) GRCh38 UCSC
7: 6043443 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161t1:c.251-20T>G
NC_000007.13:g.6043443A>C
NC_000007.14:g.6003812A>C
... more HGVS
Protein change
-
Other names
IVS3-20T>G
Canonical SPDI
NC_000007.14:6003811:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00081
Trans-Omics for Precision Medicine (TOPMed) 0.00133
The Genome Aggregation Database (gnomAD) 0.00096
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00081
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00159
Links
ClinGen: CA011617
dbSNP: rs149343081
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Apr 28, 2015 RCV000115689.8
Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 14, 2020 RCV000417396.5
Likely benign 2 criteria provided, single submitter Feb 14, 2017 RCV000679359.3
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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
3060 3125

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 29, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000149598.7
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Nov 18, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000187123.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Likely benign
(Apr 28, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686185.1
Submitted: (Oct 26, 2017)
Evidence details
Likely benign
(Feb 14, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000806209.1
Submitted: (Jan 29, 2018)
Evidence details
Likely benign
(Jul 14, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918046.3
Submitted: (Aug 06, 2020)
Evidence details
Comment:
Variant summary: PMS2 c.251-20T>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001740970.3
Submitted: (Sep 02, 2021)
Evidence details

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.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs149343081...

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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 Sep 07, 2021