rs2228396
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001290043.2(TAP2):c.1693G>A(p.Ala565Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0895 in 1,613,076 control chromosomes in the GnomAD database, including 7,097 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001290043.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAP2 | NM_001290043.2 | c.1693G>A | p.Ala565Thr | missense_variant | 10/12 | ENST00000374897.4 | NP_001276972.1 | |
TAP2 | NM_018833.3 | c.1693G>A | p.Ala565Thr | missense_variant | 10/12 | NP_061313.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000374897.4 | c.1693G>A | p.Ala565Thr | missense_variant | 10/12 | 1 | NM_001290043.2 | ENSP00000364032.3 | ||
ENSG00000250264 | ENST00000452392.2 | c.1693G>A | p.Ala565Thr | missense_variant | 10/15 | 2 | ENSP00000391806.2 |
Frequencies
GnomAD3 genomes AF: 0.0916 AC: 13940AN: 152142Hom.: 722 Cov.: 33
GnomAD3 exomes AF: 0.0800 AC: 19729AN: 246668Hom.: 930 AF XY: 0.0749 AC XY: 10063AN XY: 134434
GnomAD4 exome AF: 0.0892 AC: 130356AN: 1460816Hom.: 6373 Cov.: 72 AF XY: 0.0862 AC XY: 62679AN XY: 726718
GnomAD4 genome AF: 0.0918 AC: 13976AN: 152260Hom.: 724 Cov.: 33 AF XY: 0.0896 AC XY: 6671AN XY: 74454
ClinVar
Submissions by phenotype
MHC class I deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at