NM_001018005.2(TPM1):c.375-3C>T AND not specified

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Aug 19, 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:: RCV000154861.20

Allele description [Variation Report for NM_001018005.2(TPM1):c.375-3C>T]

NM_001018005.2(TPM1):c.375-3C>T

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.375-3C>T

HGVS:

NC_000015.10:g.63059560C>T
NG_007557.1:g.21922C>T
NM_000366.6:c.375-3C>T
NM_001018004.2:c.375-3C>T
NM_001018005.2:c.375-3C>TMANE SELECT
NM_001018006.2:c.375-3C>T
NM_001018007.2:c.375-3C>T
NM_001018008.2:c.267-3C>T
NM_001018020.2:c.375-3C>T
NM_001301244.2:c.375-3C>T
NM_001301289.2:c.267-3C>T
NM_001330344.2:c.267-3C>T
NM_001330346.2:c.267-3C>T
NM_001330351.2:c.267-3C>T
NM_001365776.1:c.375-3C>T
NM_001365777.1:c.375-3C>T
NM_001365778.1:c.501-3C>T
NM_001365779.1:c.375-3C>T
NM_001365780.1:c.267-3C>T
NM_001365781.2:c.267-3C>T
NM_001365782.1:c.267-3C>T
LRG_387t1:c.375-3C>T
LRG_387:g.21922C>T
NC_000015.9:g.63351759C>T
NM_000366.5:c.375-3C>T
NM_001018005.1:c.375-3C>T

Links:

dbSNP: rs202228866

NCBI 1000 Genomes Browser:

rs202228866

Molecular consequence:

NM_000366.6:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018004.2:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018005.2:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018006.2:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018007.2:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018008.2:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001018020.2:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001301244.2:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001301289.2:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001330344.2:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001330346.2:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001330351.2:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365776.1:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365777.1:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365778.1:c.501-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365779.1:c.375-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365780.1:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365781.2:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001365782.1:c.267-3C>T - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000204543	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Aug 26, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000264263	Blueprint Genetics	criteria provided, single submitter (Variant Classification)	Likely benign (Nov 10, 2015)	germline	clinical testing	Citation Link,
SCV000514947	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Mar 17, 2015)	germline	clinical testing	Citation Link,
SCV001920309	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
SCV001926800	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV004038012	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Aug 19, 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	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	2	2	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000204543.5

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

Description

c.375-3C>T in intron 3 of TPM1: This variant is not expected to have clinical si gnificance because it does not cause the splice site sequence to diverge from co nsensus. It has been identified in 2/8600 of European American chromosomes by th e NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs202 228866).

#	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		2	not provided	2	not provided

From Blueprint Genetics, SCV000264263.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing (GTR000519366.3)	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	(GTR000519366.3)	1	not provided	not provided	not provided

From GeneDx, SCV000514947.4

#	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 Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001920309.1

#	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 Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001926800.1

#	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, SCV004038012.1

#	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: Oct 8, 2024

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