Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: APC vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000038.6(APC):c.5038C>T (p.Gln1680Ter)

CA10578390

230520 (ClinVar)

Gene: APC
Condition: familial adenomatous polyposis 1
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 05f45393-7afc-483e-bc11-5723e575bad1
Approved on: 2025-05-19
Published on: 2025-05-19

HGVS expressions

NM_000038.6:c.5038C>T
NM_000038.6(APC):c.5038C>T (p.Gln1680Ter)
NC_000005.10:g.112840632C>T
CM000667.2:g.112840632C>T
NC_000005.9:g.112176329C>T
CM000667.1:g.112176329C>T
NC_000005.8:g.112204228C>T
NG_008481.4:g.153112C>T
ENST00000504915.3:c.5092C>T
ENST00000505350.2:c.*5044C>T
ENST00000507379.6:c.4984C>T
ENST00000509732.6:c.5038C>T
ENST00000512211.7:c.5038C>T
ENST00000257430.9:c.5038C>T
ENST00000257430.8:c.5038C>T
ENST00000508376.6:c.5038C>T
ENST00000508624.5:c.*4360C>T
ENST00000520401.1:c.230+11660C>T
NM_000038.5:c.5038C>T
NM_001127510.2:c.5038C>T
NM_001127511.2:c.4984C>T
NM_001354895.1:c.5038C>T
NM_001354896.1:c.5092C>T
NM_001354897.1:c.5068C>T
NM_001354898.1:c.4963C>T
NM_001354899.1:c.4954C>T
NM_001354900.1:c.4915C>T
NM_001354901.1:c.4861C>T
NM_001354902.1:c.4765C>T
NM_001354903.1:c.4735C>T
NM_001354904.1:c.4660C>T
NM_001354905.1:c.4558C>T
NM_001354906.1:c.4189C>T
NM_001127510.3:c.5038C>T
NM_001127511.3:c.4984C>T
NM_001354895.2:c.5038C>T
NM_001354896.2:c.5092C>T
NM_001354897.2:c.5068C>T
NM_001354898.2:c.4963C>T
NM_001354899.2:c.4954C>T
NM_001354900.2:c.4915C>T
NM_001354901.2:c.4861C>T
NM_001354902.2:c.4765C>T
NM_001354903.2:c.4735C>T
NM_001354904.2:c.4660C>T
NM_001354905.2:c.4558C>T
NM_001354906.2:c.4189C>T
More

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for APC Version 2.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP
The NM_000038.6(APC):c.5038C>T (p.Gln1680Ter) variant in APC is a nonsense variant located between codon 49 and 2645 and predicted to cause a premature stop codon in exon 16 in a gene in which loss-of-function is an established disease mechanism (PVS1). The variant has been reported in 1 proband with a colorectal cancer/polyposis associated phenotype not meeting phenotypic criteria (PS4 not met; Ambry Genetics). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Likely Pathogenic for autosomal-dominant inherited FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP: criteria PVS1 and PM2_Supporting applied (VCEP specifications version v2.1.0; date of approval 11/24/2023).
Met criteria codes
PVS1
The NM_000038.6(APC):c.5038C>T (p.Gln1680Ter) variant in APC is a nonsense variant located between codon 49 and 2645 and predicted to cause a premature stop codon in exon 16 in a gene in which loss-of-function is an established disease mechanism (PVS1).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS4
The variant has been reported in 1 proband with a colorectal cancer/polyposis associated phenotype not meeting phenotypic criteria (PS4 not met; Ambry Genetics).
Curation History
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