NM_000038.6(APC):c.7647T>A (p.Arg2549=) AND Familial adenomatous polyposis 1

Germline classification:: Benign/Likely benign (2 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:: RCV003776419.3

Allele description [Variation Report for NM_000038.6(APC):c.7647T>A (p.Arg2549=)]

NM_000038.6(APC):c.7647T>A (p.Arg2549=)

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.7647T>A (p.Arg2549=)

HGVS:

NC_000005.10:g.112843241T>A
NG_008481.4:g.155721T>A
NM_000038.6:c.7647T>AMANE SELECT
NM_001127510.3:c.7647T>A
NM_001127511.3:c.7593T>A
NM_001354895.2:c.7647T>A
NM_001354896.2:c.7701T>A
NM_001354897.2:c.7677T>A
NM_001354898.2:c.7572T>A
NM_001354899.2:c.7563T>A
NM_001354900.2:c.7524T>A
NM_001354901.2:c.7470T>A
NM_001354902.2:c.7374T>A
NM_001354903.2:c.7344T>A
NM_001354904.2:c.7269T>A
NM_001354905.2:c.7167T>A
NM_001354906.2:c.6798T>A
NM_001407446.1:c.7731T>A
NM_001407447.1:c.7701T>A
NM_001407448.1:c.7701T>A
NM_001407449.1:c.7701T>A
NM_001407450.1:c.7647T>A
NM_001407451.1:c.7626T>A
NM_001407452.1:c.7617T>A
NM_001407453.1:c.7470T>A
NM_001407454.1:c.7398T>A
NM_001407455.1:c.7398T>A
NM_001407456.1:c.7398T>A
NM_001407457.1:c.7398T>A
NM_001407458.1:c.7344T>A
NM_001407459.1:c.7344T>A
NM_001407460.1:c.7344T>A
NM_001407467.1:c.7260T>A
NM_001407469.1:c.7260T>A
NM_001407470.1:c.6798T>A
NM_001407471.1:c.6495T>A
NM_001407472.1:c.6495T>A
NP_000029.2:p.Arg2549=
NP_000029.2:p.Arg2549=
NP_001120982.1:p.Arg2549=
NP_001120982.1:p.Arg2549=
NP_001120983.1:p.Arg2549=
NP_001120983.2:p.Arg2531=
NP_001341824.1:p.Arg2549=
NP_001341825.1:p.Arg2567=
NP_001341826.1:p.Arg2559=
NP_001341827.1:p.Arg2524=
NP_001341828.1:p.Arg2521=
NP_001341829.1:p.Arg2508=
NP_001341830.1:p.Arg2490=
NP_001341831.1:p.Arg2458=
NP_001341832.1:p.Arg2448=
NP_001341833.1:p.Arg2423=
NP_001341834.1:p.Arg2389=
NP_001341835.1:p.Arg2266=
NP_001394375.1:p.Arg2577=
NP_001394376.1:p.Arg2567=
NP_001394377.1:p.Arg2567=
NP_001394378.1:p.Arg2567=
NP_001394379.1:p.Arg2549=
NP_001394380.1:p.Arg2542=
NP_001394381.1:p.Arg2539=
NP_001394382.1:p.Arg2490=
NP_001394383.1:p.Arg2466=
NP_001394384.1:p.Arg2466=
NP_001394385.1:p.Arg2466=
NP_001394386.1:p.Arg2466=
NP_001394387.1:p.Arg2448=
NP_001394388.1:p.Arg2448=
NP_001394389.1:p.Arg2448=
NP_001394396.1:p.Arg2420=
NP_001394398.1:p.Arg2420=
NP_001394399.1:p.Arg2266=
NP_001394400.1:p.Arg2165=
NP_001394401.1:p.Arg2165=
LRG_130t1:c.7647T>A
LRG_130t2:c.7647T>A
LRG_130t3:c.7647T>A
LRG_130:g.155721T>A
LRG_130p1:p.Arg2549=
LRG_130p2:p.Arg2549=
LRG_130p3:p.Arg2549=
NC_000005.9:g.112178938T>A
NM_000038.4:c.7647T>A
NM_000038.5:c.7647T>A
NM_001127510.1:c.7647T>A
NM_001127511.1:c.7647T>A
NR_176365.1:n.7482T>A
NR_176366.1:n.7901T>A

Molecular consequence:

NR_176365.1:n.7482T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.7901T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000038.6:c.7647T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127510.3:c.7647T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127511.3:c.7593T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354895.2:c.7647T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354896.2:c.7701T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354897.2:c.7677T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354898.2:c.7572T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354899.2:c.7563T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354900.2:c.7524T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354901.2:c.7470T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354902.2:c.7374T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354903.2:c.7344T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354904.2:c.7269T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354905.2:c.7167T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354906.2:c.6798T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407446.1:c.7731T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407447.1:c.7701T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407448.1:c.7701T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407449.1:c.7701T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407450.1:c.7647T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407451.1:c.7626T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407452.1:c.7617T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407453.1:c.7470T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407454.1:c.7398T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407455.1:c.7398T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407456.1:c.7398T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407457.1:c.7398T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407458.1:c.7344T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407459.1:c.7344T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407460.1:c.7344T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407467.1:c.7260T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407469.1:c.7260T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407470.1:c.6798T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407471.1:c.6495T>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407472.1:c.6495T>A - synonymous variant - [Sequence Ontology: SO:0001819]

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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B12D protein [Arabidopsis thaliana]
B12D protein [Arabidopsis thaliana]
gi|15230104|ref|NP_189632.1|

Protein
Linkage Disequilibrium
Linkage Disequilibrium
Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected ...<br/>Year introduced: 1990

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004677760	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Nov 21, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005083564	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

SCV004677760

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Nov 21, 2023)

germline

clinical testing

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

SCV005083564

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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004677760.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV005083564.1

#	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 is a silent/synonymous amino acid change and it is not expected to impact splicing.

#	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: Sep 29, 2024

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