NM_152263.4(TPM3):c.92A>C (p.Lys31Thr) AND not specified

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: May 13, 2015
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:: RCV000194376.13

Allele description [Variation Report for NM_152263.4(TPM3):c.92A>C (p.Lys31Thr)]

NM_152263.4(TPM3):c.92A>C (p.Lys31Thr)

Gene:

TPM3:tropomyosin 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_152263.4(TPM3):c.92A>C (p.Lys31Thr)

HGVS:

NC_000001.11:g.154191927T>G
NG_008621.1:g.5207A>C
NM_001364679.2:c.92A>C
NM_001364680.2:c.92A>C
NM_001364681.2:c.92A>C
NM_001364682.1:c.92A>C
NM_152263.4:c.92A>CMANE SELECT
NP_001351608.1:p.Lys31Thr
NP_001351609.1:p.Lys31Thr
NP_001351610.1:p.Lys31Thr
NP_001351611.1:p.Lys31Thr
NP_689476.2:p.Lys31Thr
LRG_681t2:c.92A>C
LRG_681:g.5207A>C
LRG_681p2:p.Lys31Thr
NC_000001.10:g.154164403T>G
NM_152263.2:c.92A>C
NM_152263.3:c.92A>C
NR_103460.2:n.174A>C

Protein change:

K31T

Links:

dbSNP: rs62000429

NCBI 1000 Genomes Browser:

rs62000429

Molecular consequence:

NM_001364679.2:c.92A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001364680.2:c.92A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001364681.2:c.92A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001364682.1:c.92A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_152263.4:c.92A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_103460.2:n.174A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000249173	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (May 13, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000269885	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Nov 24, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000249173

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(May 13, 2015)

germline

clinical testing

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

SCV000269885

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Nov 24, 2014)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000249173.1

#	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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269885.3

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

Description

Lys31Thr in exon 1 of TPM3: This variant is not expected to have clinical signif icance because it has been identified in 1.9% (81/4196) of African American chro mosomes from a broad population by the NHLBI Exome Sequencing Project (http://ev s.gs.washington.edu/EVS; dbSNP rs62000429).

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

Last Updated: Oct 13, 2024

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