NM_000038.6(APC):c.7504G>A (p.Gly2502Ser) AND Familial adenomatous polyposis 1

Germline classification:: Benign (3 submissions)
Last evaluated:: Apr 10, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003315545.11

Allele description [Variation Report for NM_000038.6(APC):c.7504G>A (p.Gly2502Ser)]

NM_000038.6(APC):c.7504G>A (p.Gly2502Ser)

Gene:

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.7504G>A (p.Gly2502Ser)

Other names:

p.G2502S:GGT>AGT; CCDS4107.1:c.7504G>A

HGVS:

NC_000005.10:g.112843098G>A
NG_008481.4:g.155578G>A
NM_000038.6:c.7504G>AMANE SELECT
NM_001127510.3:c.7504G>A
NM_001127511.3:c.7450G>A
NM_001354895.2:c.7504G>A
NM_001354896.2:c.7558G>A
NM_001354897.2:c.7534G>A
NM_001354898.2:c.7429G>A
NM_001354899.2:c.7420G>A
NM_001354900.2:c.7381G>A
NM_001354901.2:c.7327G>A
NM_001354902.2:c.7231G>A
NM_001354903.2:c.7201G>A
NM_001354904.2:c.7126G>A
NM_001354905.2:c.7024G>A
NM_001354906.2:c.6655G>A
NP_000029.2:p.Gly2502Ser
NP_000029.2:p.Gly2502Ser
NP_001120982.1:p.Gly2502Ser
NP_001120983.2:p.Gly2484Ser
NP_001341824.1:p.Gly2502Ser
NP_001341825.1:p.Gly2520Ser
NP_001341826.1:p.Gly2512Ser
NP_001341827.1:p.Gly2477Ser
NP_001341828.1:p.Gly2474Ser
NP_001341829.1:p.Gly2461Ser
NP_001341830.1:p.Gly2443Ser
NP_001341831.1:p.Gly2411Ser
NP_001341832.1:p.Gly2401Ser
NP_001341833.1:p.Gly2376Ser
NP_001341834.1:p.Gly2342Ser
NP_001341835.1:p.Gly2219Ser
LRG_130t1:c.7504G>A
LRG_130:g.155578G>A
LRG_130p1:p.Gly2502Ser
NC_000005.9:g.112178795G>A
NM_000038.4:c.7504G>A
NM_000038.5:c.7504G>A
NM_001127510.2:c.7504G>A
NM_001127511.2:c.7450G>A
P25054:p.Gly2502Ser
p.G2502S

Protein change:

G2219S

Links:

UniProtKB: P25054#VAR_005055; dbSNP: rs2229995

NCBI 1000 Genomes Browser:

rs2229995

Molecular consequence:

NM_000038.6:c.7504G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7504G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7450G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7504G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7558G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7534G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7429G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7420G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7381G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7327G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7231G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7201G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7126G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7024G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6655G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial adenomatous polyposis 1 (FAP1)
Synonyms:: POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:: MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000153849	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004017538	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005084437	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Benign (Apr 10, 2024)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000153849

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Feb 1, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004017538

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 7, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005084437

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Benign
(Apr 10, 2024)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000153849.11

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004017538.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV005084437.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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