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NM_000038.6(APC):c.6387G>A (p.Ser2129=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 8, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000183971.11
Variation ID:
183971
Description:
single nucleotide variant
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NM_000038.6(APC):c.6387G>A (p.Ser2129=)

Allele ID
182443
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q22.2
Genomic location
5: 112841981 (GRCh38) GRCh38 UCSC
5: 112177678 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_130:g.154461G>A
NC_000005.10:g.112841981G>A
NC_000005.9:g.112177678G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:112841980:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00009
The Genome Aggregation Database (gnomAD) 0.00004
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00028
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Links
ClinGen: CA011157
dbSNP: rs374310157
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 May 3, 2016 RCV000163062.3
Benign 2 criteria provided, multiple submitters, no conflicts Jan 26, 2017 RCV000589653.6
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000293113.2
Benign 1 criteria provided, single submitter Jan 20, 2020 RCV000508036.2
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV001083836.2
Likely benign 1 no assertion criteria provided - RCV001355704.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APC Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
9017 9051

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 09, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213556.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
APC-Associated Polyposis Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000452034.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000252591.9
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 03, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000681797.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Jan 26, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694091.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The APC c.6387G>A (p.Ser2129Ser) variant causes a synonymous change involving a non-conserved nucleotide, 4/5 splice prediction tools predict no significant impact on normal … (more)
Benign
(Jan 20, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000600124.2
Submitted: (Dec 31, 2020)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001838322.1
Submitted: (Sep 08, 2021)
Evidence details
Likely 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: SCV001550660.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The APC p.Ser2129= variant was not identified in the literature nor was it identified in the COGR, Cosmic, LOVD 3.0, UMD-LSDB, or in Zhejiang University … (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.

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 rs374310157...

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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 Nov 27, 2021