17-10825534-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001101387.2(PIRT):c.112G>A(p.Glu38Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000754 in 1,459,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIRT | ENST00000580256.3 | c.112G>A | p.Glu38Lys | missense_variant | Exon 2 of 2 | 2 | NM_001101387.2 | ENSP00000462046.1 | ||
ENSG00000284876 | ENST00000643787.1 | n.150+12411G>A | intron_variant | Intron 1 of 2 | ||||||
ENSG00000285220 | ENST00000647474.1 | n.269-22358C>T | intron_variant | Intron 3 of 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000820 AC: 2AN: 244038Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132392
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1459484Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 6AN XY: 725752
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.112G>A (p.E38K) 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 112, causing the glutamic acid (E) at amino acid position 38 to be replaced by a lysine (K). 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