rs144951468
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_000593.6(TAP1):c.1593C>T(p.Gly531=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000194 in 1,611,186 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G531G) has been classified as Likely benign.
Frequency
Consequence
NM_000593.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAP1 | NM_000593.6 | c.1593C>T | p.Gly531= | synonymous_variant | 8/11 | ENST00000354258.5 | |
TAP1 | NM_001292022.2 | c.990C>T | p.Gly330= | synonymous_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP1 | ENST00000354258.5 | c.1593C>T | p.Gly531= | synonymous_variant | 8/11 | 1 | NM_000593.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000220 AC: 53AN: 240774Hom.: 1 AF XY: 0.000281 AC XY: 37AN XY: 131460
GnomAD4 exome AF: 0.000160 AC: 233AN: 1458836Hom.: 1 Cov.: 32 AF XY: 0.000182 AC XY: 132AN XY: 725604
GnomAD4 genome AF: 0.000519 AC: 79AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000550 AC XY: 41AN XY: 74502
ClinVar
Submissions by phenotype
MHC class I deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at