rs375389015
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000354258.5(TAP1):c.19C>T(p.Pro7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000577 in 1,611,936 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000354258.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAP1 | NM_000593.6 | c.19C>T | p.Pro7Ser | missense_variant | 1/11 | ENST00000354258.5 | NP_000584.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAP1 | ENST00000354258.5 | c.19C>T | p.Pro7Ser | missense_variant | 1/11 | 1 | NM_000593.6 | ENSP00000346206 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000336 AC: 8AN: 237796Hom.: 0 AF XY: 0.0000535 AC XY: 7AN XY: 130958
GnomAD4 exome AF: 0.0000507 AC: 74AN: 1459714Hom.: 2 Cov.: 32 AF XY: 0.0000537 AC XY: 39AN XY: 726218
GnomAD4 genome AF: 0.000125 AC: 19AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74364
ClinVar
Submissions by phenotype
MHC class I deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 07, 2022 | This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 67 of the TAP1 protein (p.Pro67Ser). This variant is present in population databases (rs375389015, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 582649). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at