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NM_000038.6(APC):c.3048T>C (p.Asp1016=) AND Familial adenomatous polyposis 1

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Mar 18, 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:
RCV003538796.2

Allele description

NM_000038.6(APC):c.3048T>C (p.Asp1016=)

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.3048T>C (p.Asp1016=)
HGVS:
  • NC_000005.10:g.112838642T>C
  • NG_008481.4:g.151122T>C
  • NM_000038.6:c.3048T>CMANE SELECT
  • NM_001127510.3:c.3048T>C
  • NM_001127511.3:c.2994T>C
  • NM_001354895.2:c.3048T>C
  • NM_001354896.2:c.3102T>C
  • NM_001354897.2:c.3078T>C
  • NM_001354898.2:c.2973T>C
  • NM_001354899.2:c.2964T>C
  • NM_001354900.2:c.2925T>C
  • NM_001354901.2:c.2871T>C
  • NM_001354902.2:c.2775T>C
  • NM_001354903.2:c.2745T>C
  • NM_001354904.2:c.2670T>C
  • NM_001354905.2:c.2568T>C
  • NM_001354906.2:c.2199T>C
  • NP_000029.2:p.Asp1016=
  • NP_001120982.1:p.Asp1016=
  • NP_001120983.2:p.Asp998=
  • NP_001341824.1:p.Asp1016=
  • NP_001341825.1:p.Asp1034=
  • NP_001341826.1:p.Asp1026=
  • NP_001341827.1:p.Asp991=
  • NP_001341828.1:p.Asp988=
  • NP_001341829.1:p.Asp975=
  • NP_001341830.1:p.Asp957=
  • NP_001341831.1:p.Asp925=
  • NP_001341832.1:p.Asp915=
  • NP_001341833.1:p.Asp890=
  • NP_001341834.1:p.Asp856=
  • NP_001341835.1:p.Asp733=
  • LRG_130:g.151122T>C
  • NC_000005.9:g.112174339T>C
  • NM_000038.5:c.3048T>C
Links:
dbSNP: rs2149883068
NCBI 1000 Genomes Browser:
rs2149883068
Molecular consequence:
  • NM_000038.6:c.3048T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.3048T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.2994T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.3048T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.3102T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.3078T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.2973T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.2964T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.2925T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.2871T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.2775T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.2745T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.2670T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.2568T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.2199T>C - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001686628Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Jun 27, 2023) 		germlineclinical testing

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

SCV004933238Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))		Benign
(Mar 18, 2024) 		unknownclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV001686628.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Myriad Genetics, Inc., SCV004933238.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 2, 2024