NM_001018005.2(TPM1):c.486T>C (p.Tyr162=) AND not specified

Germline classification:: Benign (7 submissions)
Last evaluated:: Apr 10, 2023
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:: RCV000036337.21

Allele description [Variation Report for NM_001018005.2(TPM1):c.486T>C (p.Tyr162=)]

NM_001018005.2(TPM1):c.486T>C (p.Tyr162=)

Gene:

TPM1:tropomyosin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q22.2

Genomic location:

Preferred name:

NM_001018005.2(TPM1):c.486T>C (p.Tyr162=)

Other names:

p.Y162Y:TAT>TAC

HGVS:

NC_000015.10:g.63059674T>C
NG_007557.1:g.22036T>C
NM_000366.6:c.486T>C
NM_001018004.2:c.486T>C
NM_001018005.2:c.486T>CMANE SELECT
NM_001018006.2:c.486T>C
NM_001018007.2:c.486T>C
NM_001018008.2:c.378T>C
NM_001018020.2:c.486T>C
NM_001301244.2:c.486T>C
NM_001301289.2:c.378T>C
NM_001330344.2:c.378T>C
NM_001330346.2:c.378T>C
NM_001330351.2:c.378T>C
NM_001365776.1:c.486T>C
NM_001365777.1:c.486T>C
NM_001365778.1:c.612T>C
NM_001365779.1:c.486T>C
NM_001365780.1:c.378T>C
NM_001365781.2:c.378T>C
NM_001365782.1:c.378T>C
NP_000357.3:p.Tyr162=
NP_001018004.1:p.Tyr162=
NP_001018005.1:p.Tyr162=
NP_001018006.1:p.Tyr162=
NP_001018007.1:p.Tyr162=
NP_001018008.1:p.Tyr126=
NP_001018020.1:p.Tyr162=
NP_001288173.1:p.Tyr162=
NP_001288218.1:p.Tyr126=
NP_001317273.1:p.Tyr126=
NP_001317275.1:p.Tyr126=
NP_001317280.1:p.Tyr126=
NP_001352705.1:p.Tyr162=
NP_001352706.1:p.Tyr162=
NP_001352707.1:p.Tyr204=
NP_001352708.1:p.Tyr162=
NP_001352709.1:p.Tyr126=
NP_001352710.1:p.Tyr126=
NP_001352711.1:p.Tyr126=
LRG_387t1:c.486T>C
LRG_387:g.22036T>C
LRG_387p1:p.Tyr162=
NC_000015.9:g.63351873T>C
NM_000366.5:c.486T>C
NM_001018005.1:c.486T>C
NM_001018020.1:c.486T>C
c.486T>C
p.(=)
p.Tyr162Tyr

Links:

Leiden Muscular Dystrophy (TPM1): TPM1_00020; dbSNP: rs11558747

NCBI 1000 Genomes Browser:

rs11558747

Molecular consequence:

NM_000366.6:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001018004.2:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001018005.2:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001018006.2:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001018007.2:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001018008.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001018020.2:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001301244.2:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001301289.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330344.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330346.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330351.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365776.1:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365777.1:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365778.1:c.612T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365779.1:c.486T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365780.1:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365781.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001365782.1:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Functional consequence:

probably no functional consequence

Observations:

516

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
SCV000059989	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (May 10, 2016)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24183960, 24033266
SCV000169033	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jun 27, 2011)	germline	clinical testing	Citation Link,
SCV000305849	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001924768	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001958374	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV001973183	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV003929101	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Apr 10, 2023)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	518	516	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

DNA sequence capture and next-generation sequencing for the molecular diagnosis of genetic cardiomyopathies.

D'Argenio V, Frisso G, Precone V, Boccia A, Fienga A, Pacileo G, Limongelli G, Paolella G, Calabrò R, Salvatore F.

J Mol Diagn. 2014 Jan;16(1):32-44. doi: 10.1016/j.jmoldx.2013.07.008. Epub 2013 Oct 31.

PubMed [citation]

PMID:: 24183960

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

See all PubMed Citations (3)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000059989.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	518	not provided	not provided	clinical testing	PubMed (2)

Description

p.Tyr162Tyr in exon 4 of TPM1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 8% (5101/66566) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs11558747).

#	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		518	not provided	516	not provided

From GeneDx, SCV000169033.11

#	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 likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 PreventionGenetics, part of Exact Sciences, SCV000305849.1

#	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 Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001924768.1

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

#	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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001958374.1

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

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001973183.1

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

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003929101.1

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

#	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: May 7, 2024

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