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NM_181486.4(TBX5):c.55G>T (p.Ala19Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Nov 30, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000264111.6
Variation ID:
264111
Description:
single nucleotide variant
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NM_181486.4(TBX5):c.55G>T (p.Ala19Ser)

Allele ID
258718
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q24.21
Genomic location
12: 114403844 (GRCh38) GRCh38 UCSC
12: 114841649 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.114841649C>A
NC_000012.12:g.114403844C>A
NG_007373.1:g.9599G>T
... more HGVS
Protein change
A19S
Other names
-
Canonical SPDI
NC_000012.12:114403843:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00054
Trans-Omics for Precision Medicine (TOPMed) 0.00072
Exome Aggregation Consortium (ExAC) 0.00027
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
1000 Genomes Project 0.00140
Links
ClinGen: CA6809736
dbSNP: rs200461617
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jun 17, 2019 RCV000244681.1
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000292317.2
Uncertain significance 1 criteria provided, single submitter Jul 11, 2017 RCV000596892.4
Likely benign 1 criteria provided, single submitter Dec 31, 2019 RCV001088685.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TBX5 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
356 374

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Holt-Oram syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000376513.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Jun 17, 2019)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000319805.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other data supporting benign classification
Uncertain significance
(Jul 11, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000702672.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Aortic valve disease 2
Allele origin: germline
Invitae
Accession: SCV001004789.2
Submitted: (Jan 29, 2020)
Evidence details

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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TBX5 - - - -

Text-mined citations for rs200461617...

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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 Oct 30, 2021