rs2856992
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001290043.2(TAP2):c.1161G>A(p.Val387Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 1,612,722 control chromosomes in the GnomAD database, including 570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001290043.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000374897.4 | c.1161G>A | p.Val387Val | synonymous_variant | Exon 7 of 12 | 1 | NM_001290043.2 | ENSP00000364032.3 | ||
ENSG00000250264 | ENST00000452392.2 | c.1161G>A | p.Val387Val | synonymous_variant | Exon 7 of 15 | 2 | ENSP00000391806.2 |
Frequencies
GnomAD3 genomes AF: 0.0204 AC: 3104AN: 152202Hom.: 46 Cov.: 32
GnomAD3 exomes AF: 0.0145 AC: 3561AN: 245660Hom.: 45 AF XY: 0.0139 AC XY: 1863AN XY: 133854
GnomAD4 exome AF: 0.0242 AC: 35398AN: 1460402Hom.: 524 Cov.: 32 AF XY: 0.0230 AC XY: 16727AN XY: 726462
GnomAD4 genome AF: 0.0204 AC: 3105AN: 152320Hom.: 46 Cov.: 32 AF XY: 0.0185 AC XY: 1378AN XY: 74494
ClinVar
Submissions by phenotype
MHC class I deficiency Benign:1
- -
TAP2-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at