chr6-149378603-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001292034.3(TAB2):c.688C>A(p.Gln230Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Q230Q) has been classified as Likely benign.
Frequency
Consequence
NM_001292034.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAB2 | NM_001292034.3 | c.688C>A | p.Gln230Lys | missense_variant | 3/7 | ENST00000637181.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAB2 | ENST00000637181.2 | c.688C>A | p.Gln230Lys | missense_variant | 3/7 | 1 | NM_001292034.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250908Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135688
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461278Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727000
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
Congenital heart defects, multiple types, 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 11, 2010 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2021 | Has been reported in a patient with biscuspid aortic valve and aortic dilation in the published literature (Theinpont et al., 2010); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 20493459) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at