17-3690443-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002561.4(P2RX5):c.517A>T(p.Thr173Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,611,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002561.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX5 | NM_002561.4 | c.517A>T | p.Thr173Ser | missense_variant | 5/12 | ENST00000225328.10 | |
P2RX5-TAX1BP3 | NR_037928.1 | n.916A>T | non_coding_transcript_exon_variant | 5/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX5 | ENST00000225328.10 | c.517A>T | p.Thr173Ser | missense_variant | 5/12 | 1 | NM_002561.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000689 AC: 17AN: 246708Hom.: 0 AF XY: 0.0000896 AC XY: 12AN XY: 133970
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459496Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 726010
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.517A>T (p.T173S) alteration is located in exon 5 (coding exon 5) of the P2RX5 gene. This alteration results from a A to T substitution at nucleotide position 517, causing the threonine (T) at amino acid position 173 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