17-10825488-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001101387.2(PIRT):c.158G>A(p.Arg53His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,613,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIRT | ENST00000580256.3 | c.158G>A | p.Arg53His | missense_variant | Exon 2 of 2 | 2 | NM_001101387.2 | ENSP00000462046.1 | ||
ENSG00000284876 | ENST00000643787.1 | n.150+12457G>A | intron_variant | Intron 1 of 2 | ||||||
ENSG00000285220 | ENST00000647474.1 | n.269-22404C>T | intron_variant | Intron 3 of 5 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152094Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248636Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134898
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461626Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727074
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.158G>A (p.R53H) 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 158, causing the arginine (R) at amino acid position 53 to be replaced by a histidine (H). 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