8-119732109-T-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_003184.4(TAF2):āc.3415A>Gā(p.Thr1139Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 1,613,892 control chromosomes in the GnomAD database, including 11,697 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAF2 | NM_003184.4 | c.3415A>G | p.Thr1139Ala | missense_variant | 26/26 | ENST00000378164.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF2 | ENST00000378164.7 | c.3415A>G | p.Thr1139Ala | missense_variant | 26/26 | 1 | NM_003184.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.166 AC: 25237AN: 152056Hom.: 4022 Cov.: 32
GnomAD3 exomes AF: 0.0943 AC: 23685AN: 251174Hom.: 2298 AF XY: 0.0913 AC XY: 12397AN XY: 135738
GnomAD4 exome AF: 0.0812 AC: 118658AN: 1461718Hom.: 7664 Cov.: 32 AF XY: 0.0819 AC XY: 59561AN XY: 727176
GnomAD4 genome AF: 0.166 AC: 25284AN: 152174Hom.: 4033 Cov.: 32 AF XY: 0.162 AC XY: 12043AN XY: 74412
ClinVar
Submissions by phenotype
TAF2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at