NM_181486.4(TBX5):c.1234G>A (p.Val412Ile) AND not provided

Clinical significance:Benign (Last evaluated: Mar 27, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000588683.3

Allele description [Variation Report for NM_181486.4(TBX5):c.1234G>A (p.Val412Ile)]

NM_181486.4(TBX5):c.1234G>A (p.Val412Ile)

Gene:
TBX5:T-box transcription factor 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.21
Genomic location:
Preferred name:
NM_181486.4(TBX5):c.1234G>A (p.Val412Ile)
HGVS:
  • NC_000012.12:g.114355855C>T
  • NG_007373.1:g.57588G>A
  • NM_000192.3:c.1234G>A
  • NM_080717.4:c.1084G>A
  • NM_181486.4:c.1234G>AMANE SELECT
  • NP_000183.2:p.Val412Ile
  • NP_542448.1:p.Val362Ile
  • NP_852259.1:p.Val412Ile
  • LRG_670t1:c.1234G>A
  • LRG_670:g.57588G>A
  • LRG_670p1:p.Val412Ile
  • NC_000012.11:g.114793660C>T
Protein change:
V362I
Links:
dbSNP: rs114124210
NCBI 1000 Genomes Browser:
rs114124210
Molecular consequence:
  • NM_000192.3:c.1234G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080717.4:c.1084G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181486.4:c.1234G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000695948Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Mar 27, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695948.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The c.1234G>A (p.Val412Ile) in TBX5 gene is a missense change that involves a conserved nucleotide and 2/4 in silico tools predict deleterious outcome. The variant is located outside of any known functional domain and no functional studies confirming deleterious effect of this change have been reported at the time of evaluation. The variant is present in the control population dataset of ExAC at a frequency of 0.0009702 (117/ 120590 chrs tested), predominantly in individuals of African descent (0.01025; 105/ 120590 chrs tested, including 2 homozygotes. The observed frequency exceed the maximum expected allele frequency for a pathogenic variant of 0.0000013. The variant is present in a control population dataset of gnomAD at a frequency of 0.0009577 (265/276692 chrs), mainly in individuals of African origin: 0.009912 (238/24012 chrs, including 2 homozygotes). This data suggest that the variant of interest may be an ethnic-specific functional polymorphism. The variant has not, to our knowledge, been reported in affected individuals via published reports or cited by reputable databases/clinical laboratories. Taking together, the variant was classified as Benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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