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]

Link to SEPIO compliant JSON-LD document

Variant: NM_000038.6(APC):c.6796_6810del (p.Thr2266_Ser2270del)

CA16042098

371858 (ClinVar)

Gene: APC

Condition: familial adenomatous polyposis 1

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 9f5fe105-afaf-4f42-b388-af9edfd2a4ee

Approved on: 2023-02-26

Published on: 2023-03-14

HGVS expressions

NM_000038.6:c.6796_6810del

NM_000038.6(APC):c.6796_6810del (p.Thr2266_Ser2270del)

NC_000005.10:g.112842390_112842404del

CM000667.2:g.112842390_112842404del

NC_000005.9:g.112178087_112178101del

CM000667.1:g.112178087_112178101del

NC_000005.8:g.112205986_112206000del

NG_008481.4:g.154870_154884del

ENST00000257430.9:c.6796_6810del

ENST00000257430.8:c.6796_6810del

ENST00000508376.6:c.6796_6810del

ENST00000508624.5:c.*6118_*6132del

ENST00000520401.1:n.230+13418_230+13432del

NM_000038.5:c.6796_6810del

NM_001127510.2:c.6796_6810del

NM_001127511.2:c.6742_6756del

NM_001354895.1:c.6796_6810del

NM_001354896.1:c.6850_6864del

NM_001354897.1:c.6826_6840del

NM_001354898.1:c.6721_6735del

NM_001354899.1:c.6712_6726del

NM_001354900.1:c.6673_6687del

NM_001354901.1:c.6619_6633del

NM_001354902.1:c.6523_6537del

NM_001354903.1:c.6493_6507del

NM_001354904.1:c.6418_6432del

NM_001354905.1:c.6316_6330del

NM_001354906.1:c.5947_5961del

NM_001127510.3:c.6796_6810del

NM_001127511.3:c.6742_6756del

NM_001354895.2:c.6796_6810del

NM_001354896.2:c.6850_6864del

NM_001354897.2:c.6826_6840del

NM_001354898.2:c.6721_6735del

NM_001354899.2:c.6712_6726del

NM_001354900.2:c.6673_6687del

NM_001354901.2:c.6619_6633del

NM_001354902.2:c.6523_6537del

NM_001354903.2:c.6493_6507del

NM_001354904.2:c.6418_6432del

NM_001354905.2:c.6316_6330del

NM_001354906.2:c.5947_5961del

Uncertain Significance

BS2_Supporting PM2_Supporting

PS3 BA1 PM4 BS3 BS1

Evidence Links 0

Expert Panel

InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP

The c.6796_6810del variant is predicted to cause a change in the length of the protein due to an in-frame deletion of 5 amino acids (p.Thr2266_Ser2270del). This variant has been observed in 3 heterozygous individuals over the age of 50 with no features of FAP or family history of FAP, which is worth 3 healthy individual points (BS2_Supporting; Invitae internal data). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Due to insufficient evidence, this variant is classified as a Variant of Uncertain Significance (VUS) for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: BS2_Supporting and PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022).

BS2_Supporting

This variant has been observed in 3 heterozygous individuals over the age of 50 with no features of FAP or family history of FAP, a condition with full penetrance at an early age (BS2_Supporting; Invitae).

PM2_Supporting

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

PS3

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BA1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PM4

Not used by InSiGHT VCEP

BS3

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

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