NM_000038.6(APC):c.7540A>G (p.Thr2514Ala) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Mar 28, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000575061.12

Allele description [Variation Report for NM_000038.6(APC):c.7540A>G (p.Thr2514Ala)]

NM_000038.6(APC):c.7540A>G (p.Thr2514Ala)

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.7540A>G (p.Thr2514Ala)

HGVS:

NC_000005.10:g.112843134A>G
NG_008481.4:g.155614A>G
NM_000038.6:c.7540A>GMANE SELECT
NM_001127510.3:c.7540A>G
NM_001127511.3:c.7486A>G
NM_001354895.2:c.7540A>G
NM_001354896.2:c.7594A>G
NM_001354897.2:c.7570A>G
NM_001354898.2:c.7465A>G
NM_001354899.2:c.7456A>G
NM_001354900.2:c.7417A>G
NM_001354901.2:c.7363A>G
NM_001354902.2:c.7267A>G
NM_001354903.2:c.7237A>G
NM_001354904.2:c.7162A>G
NM_001354905.2:c.7060A>G
NM_001354906.2:c.6691A>G
NP_000029.2:p.Thr2514Ala
NP_001120982.1:p.Thr2514Ala
NP_001120983.2:p.Thr2496Ala
NP_001341824.1:p.Thr2514Ala
NP_001341825.1:p.Thr2532Ala
NP_001341826.1:p.Thr2524Ala
NP_001341827.1:p.Thr2489Ala
NP_001341828.1:p.Thr2486Ala
NP_001341829.1:p.Thr2473Ala
NP_001341830.1:p.Thr2455Ala
NP_001341831.1:p.Thr2423Ala
NP_001341832.1:p.Thr2413Ala
NP_001341833.1:p.Thr2388Ala
NP_001341834.1:p.Thr2354Ala
NP_001341835.1:p.Thr2231Ala
LRG_130:g.155614A>G
NC_000005.9:g.112178831A>G
NM_000038.5:c.7540A>G

Protein change:

T2231A

Links:

dbSNP: rs545125246

NCBI 1000 Genomes Browser:

rs545125246

Molecular consequence:

NM_000038.6:c.7540A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7540A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7486A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7540A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7570A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7465A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7456A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7417A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7363A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7267A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7237A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7162A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7060A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6691A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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LOC129597079 [Paramacrobiotus metropolitanus]
LOC129597079 [Paramacrobiotus metropolitanus]
Gene ID:129597079

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000676379	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Mar 28, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000676379

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Mar 28, 2023)

germline

clinical testing

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

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

Citations

PubMed

Gene Sequencing for Pathogenic Variants Among Adults With Breast and Ovarian Cancer in the Caribbean.

George SHL, Donenberg T, Alexis C, DeGennaro V Jr, Dyer H, Yin S, Ali J, Butler R, Chin SN, Curling D, Lowe D, Lunn J, Turnquest T, Wharfe G, Cerbon D, Barreto-Coelho P, Schlumbrecht MP, Akbari MR, Narod SA, Hurley JE.

JAMA Netw Open. 2021 Mar 1;4(3):e210307. doi: 10.1001/jamanetworkopen.2021.0307.

PubMed [citation]

PMID:: 33646313
PMCID:: PMC7921902

Details of each submission

From Ambry Genetics, SCV000676379.6

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

Last Updated: Oct 26, 2024

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