16-1256668-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_012217.3(TPSD1):c.235G>T(p.Ala79Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_012217.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPSD1 | ENST00000211076.5 | c.235G>T | p.Ala79Ser | missense_variant | Exon 2 of 5 | 1 | NM_012217.3 | ENSP00000211076.3 | ||
TPSD1 | ENST00000397534.6 | c.214G>T | p.Ala72Ser | missense_variant | Exon 3 of 6 | 5 | ENSP00000380668.2 |
Frequencies
GnomAD3 genomes Cov.: 37
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248762Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134648
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459584Hom.: 0 Cov.: 130 AF XY: 0.00000138 AC XY: 1AN XY: 726052
GnomAD4 genome Cov.: 37
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at