6-32847132-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000593.6(TAP1):c.1976G>A(p.Arg659Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0015 in 1,612,946 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R659W) has been classified as Uncertain significance.
Frequency
Consequence
NM_000593.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAP1 | NM_000593.6 | c.1976G>A | p.Arg659Gln | missense_variant | 10/11 | ENST00000354258.5 | |
TAP1 | NM_001292022.2 | c.1373G>A | p.Arg458Gln | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP1 | ENST00000354258.5 | c.1976G>A | p.Arg659Gln | missense_variant | 10/11 | 1 | NM_000593.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000920 AC: 140AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00120 AC: 295AN: 246260Hom.: 1 AF XY: 0.00118 AC XY: 158AN XY: 134250
GnomAD4 exome AF: 0.00156 AC: 2282AN: 1460620Hom.: 2 Cov.: 32 AF XY: 0.00151 AC XY: 1096AN XY: 726630
GnomAD4 genome AF: 0.000919 AC: 140AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000792 AC XY: 59AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
MHC class I deficiency Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 02, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
TAP1 deficiency, somatic Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 1996 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at