12-6453127-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000266556.8(TAPBPL):c.125C>T(p.Ala42Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,588,640 control chromosomes in the GnomAD database, including 61,467 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000266556.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAPBPL | NM_018009.5 | c.125C>T | p.Ala42Val | missense_variant | 2/7 | ENST00000266556.8 | NP_060479.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAPBPL | ENST00000266556.8 | c.125C>T | p.Ala42Val | missense_variant | 2/7 | 1 | NM_018009.5 | ENSP00000266556 | P1 |
Frequencies
GnomAD3 genomes AF: 0.235 AC: 35659AN: 151670Hom.: 4563 Cov.: 31
GnomAD3 exomes AF: 0.261 AC: 54654AN: 209442Hom.: 7530 AF XY: 0.269 AC XY: 30201AN XY: 112112
GnomAD4 exome AF: 0.279 AC: 400519AN: 1436850Hom.: 56905 Cov.: 51 AF XY: 0.280 AC XY: 199643AN XY: 712214
GnomAD4 genome AF: 0.235 AC: 35675AN: 151790Hom.: 4562 Cov.: 31 AF XY: 0.236 AC XY: 17517AN XY: 74142
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at