17-10825441-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001101387.2(PIRT):c.205G>A(p.Gly69Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000239 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001101387.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIRT | ENST00000580256.3 | c.205G>A | p.Gly69Ser | missense_variant | Exon 2 of 2 | 2 | NM_001101387.2 | ENSP00000462046.1 | ||
ENSG00000284876 | ENST00000643787.1 | n.150+12504G>A | intron_variant | Intron 1 of 2 | ||||||
ENSG00000285220 | ENST00000647474.1 | n.269-22451C>T | intron_variant | Intron 3 of 5 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152026Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000843 AC: 21AN: 248972Hom.: 0 AF XY: 0.0000963 AC XY: 13AN XY: 135060
GnomAD4 exome AF: 0.000248 AC: 363AN: 1461700Hom.: 0 Cov.: 30 AF XY: 0.000234 AC XY: 170AN XY: 727134
GnomAD4 genome AF: 0.000151 AC: 23AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.205G>A (p.G69S) alteration is located in exon 2 (coding exon 1) of the PIRT gene. This alteration results from a G to A substitution at nucleotide position 205, causing the glycine (G) at amino acid position 69 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at