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NM_001256317.3(TMPRSS3):c.268G>A (p.Ala90Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Feb 20, 2020)
Last evaluated:
Oct 15, 2018
Accession:
VCV000046107.5
Variation ID:
46107
Description:
single nucleotide variant
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NM_001256317.3(TMPRSS3):c.268G>A (p.Ala90Thr)

Allele ID
55272
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
21q22.3
Genomic location
21: 42388983 (GRCh38) GRCh38 UCSC
21: 43809092 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000021.8:g.43809092C>T
NC_000021.9:g.42388983C>T
NG_011629.2:g.12109G>A
... more HGVS
Protein change
A90T
Other names
-
Canonical SPDI
NC_000021.9:42388982:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.01018 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.03095
Exome Aggregation Consortium (ExAC) 0.03300
Trans-Omics for Precision Medicine (TOPMed) 0.03333
The Genome Aggregation Database (gnomAD) 0.03880
1000 Genomes Project 0.01018
The Genome Aggregation Database (gnomAD), exomes 0.03178
The Genome Aggregation Database (gnomAD) 0.03352
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03498
Links
ClinGen: CA137696
dbSNP: rs45598239
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts Sep 8, 2017 RCV000039344.6
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 15, 2018 RCV000999777.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TMPRSS3 - - GRCh38
GRCh37
257 339

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 08, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000730617.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Benign
(Dec 16, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230403.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Oct 26, 2010)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000063028.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Ala90Thr in exon 4 of TMPRSS3: This variant has been identified in 4/178 (2.2%) probands with hearing loss (Rehm, unpublished data; Hutchin 2005) and was … (more)
Benign
(Oct 15, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 8
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000605388.2
Submitted: (Aug 05, 2019)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000314232.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 8
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001300981.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Assessment of the genetic causes of recessive childhood non-syndromic deafness in the UK - implications for genetic testing. Hutchin T Clinical genetics 2005 PMID: 16283880
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TMPRSS3 - - - -

Text-mined citations for rs45598239...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021