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NM_000038.6(APC):c.7929A>G (p.Leu2643=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Jul 4, 2021)
Last evaluated:
Apr 23, 2021
Accession:
VCV000185449.15
Variation ID:
185449
Description:
single nucleotide variant
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NM_000038.6(APC):c.7929A>G (p.Leu2643=)

Allele ID
182480
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q22.2
Genomic location
5: 112843523 (GRCh38) GRCh38 UCSC
5: 112179220 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.112843523A>G
NC_000005.9:g.112179220A>G
NG_008481.4:g.156003A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:112843522:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00011
The Genome Aggregation Database (gnomAD) 0.00032
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00009
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Links
ClinGen: CA014191
dbSNP: rs138796072
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 9, 2016 RCV000164877.2
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 26, 2020 RCV000230717.7
Benign 2 criteria provided, multiple submitters, no conflicts Apr 23, 2021 RCV000441754.2
Likely benign 1 criteria provided, single submitter May 1, 2019 RCV000858816.4
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001155674.1
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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
(Oct 03, 2016)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: unknown
Counsyl
Accession: SCV000489380.1
Submitted: (Nov 23, 2016)
Evidence details
Benign
(Apr 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000512090.4
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)
Likely benign
(Jun 25, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000215563.6
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)
Benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000282836.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Oct 09, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000681895.1
Submitted: (Oct 26, 2017)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
APC-Associated Polyposis Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001317122.1
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
(Apr 23, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001623192.1
Submitted: (May 19, 2021)
Evidence details
Likely benign
(May 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001154487.7
Submitted: (Jul 04, 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 rs138796072...

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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