19-46621402-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000960.4(PTGIR):c.1039G>T(p.Val347Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,602,022 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. V347M) has been classified as Uncertain significance.
Frequency
Consequence
NM_000960.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGIR | ENST00000291294.7 | c.1039G>T | p.Val347Leu | missense_variant | Exon 3 of 3 | 1 | NM_000960.4 | ENSP00000291294.1 | ||
PTGIR | ENST00000598865.5 | c.403G>T | p.Val135Leu | missense_variant | Exon 3 of 3 | 3 | ENSP00000470799.1 | |||
PTGIR | ENST00000594275.1 | c.310G>T | p.Val104Leu | missense_variant | Exon 3 of 3 | 3 | ENSP00000469408.1 | |||
PTGIR | ENST00000597185.1 | c.226G>T | p.Val76Leu | missense_variant | Exon 2 of 2 | 3 | ENSP00000470566.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 244926Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132604
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1449782Hom.: 0 Cov.: 33 AF XY: 0.00000139 AC XY: 1AN XY: 719344
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74380
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at