Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_000038.6(APC):c.156del (p.Gly53fs)

CA915943441

654864 (ClinVar)

Gene: APC (HGNC:324)

Condition: familial adenomatous polyposis 1 (MONDO:0021056)

Inheritance Mode: Autosomal dominant inheritance

UUID: e3c74d49-1ae8-4d1d-a295-0afa3fb40eac

Approved on: 2025-05-15

Published on: 2025-05-19

HGVS expressions

NM_000038.6:c.156del

NM_000038.6(APC):c.156del (p.Gly53fs)

NC_000005.10:g.112766346del

CM000667.2:g.112766346del

NC_000005.9:g.112102043del

CM000667.1:g.112102043del

NC_000005.8:g.112129942del

NG_008481.4:g.78826del

ENST00000502371.3:c.156del

ENST00000504915.3:c.156del

ENST00000505084.2:n.212del

ENST00000505350.2:c.*162del

ENST00000507379.6:c.186del

ENST00000509732.6:c.156del

ENST00000512211.7:c.156del

ENST00000257430.9:c.156del

ENST00000257430.8:c.156del

ENST00000505350.1:c.*162del

ENST00000507379.5:c.186del

ENST00000508376.6:c.156del

ENST00000508624.5:c.156del

ENST00000509732.5:c.156del

ENST00000512211.6:c.156del

NM_000038.5:c.156del

NM_001127510.2:c.156del

NM_001127511.2:c.186del

NM_001354895.1:c.156del

NM_001354896.1:c.156del

NM_001354897.1:c.186del

NM_001354898.1:c.81del

NM_001354899.1:c.156del

NM_001354900.1:c.-22del

NM_001354901.1:c.-22del

NM_001354902.1:c.186del

NM_001354903.1:c.156del

NM_001354904.1:c.81del

NM_001354905.1:c.-22del

NM_001354906.1:c.-880del

NM_001127510.3:c.156del

NM_001127511.3:c.186del

NM_001354895.2:c.156del

NM_001354896.2:c.156del

NM_001354897.2:c.186del

NM_001354898.2:c.81del

NM_001354899.2:c.156del

NM_001354900.2:c.-22del

NM_001354901.2:c.-22del

NM_001354902.2:c.186del

NM_001354903.2:c.156del

NM_001354904.2:c.81del

NM_001354905.2:c.-22del

NM_001354906.2:c.-880del

Likely Pathogenic

PM2_Supporting PVS1

PS4

Evidence Links 0

Expert Panel

InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP

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.156del (p.Gly53GlufsTer17) variant in APC is a frameshift variant located between codon 49 and 2645 and predicted to cause a premature stop codon in exon 3 in a gene in which loss-of-function is an established disease mechanism (PVS1). The variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant has been reported in 1 proband meeting phenotypic criteria, resulting in a total phenotype score of 0.5 points (PS4 not met; internal data Labcorp Genetics [formerly Invitae]). 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: PVS1 and PM2_Supporting (VCEP specifications version v2.1.0; date of approval 11/24/2023).

PM2_Supporting

The variant is absent from gnomAD v2.1.1 (PM2_Supporting).

PVS1

PS4

This variant has been reported in 1 proband meeting phenotypic criteria, resulting in a total phenotype score of 0.5 points (PS4 not met; internal data Labcorp Genetics [formerly Invitae]).

Curation History

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