rs779346609
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000593.6(TAP1):c.977C>T(p.Ser326Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S326Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_000593.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAP1 | NM_000593.6 | c.977C>T | p.Ser326Phe | missense_variant | 4/11 | ENST00000354258.5 | |
TAP1 | NM_001292022.2 | c.374C>T | p.Ser125Phe | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP1 | ENST00000354258.5 | c.977C>T | p.Ser326Phe | missense_variant | 4/11 | 1 | NM_000593.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246976Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134562
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460736Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 726684
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at