chrX-70259132-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002565.4(P2RY4):c.493G>A(p.Gly165Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,210,736 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002565.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RY4 | NM_002565.4 | c.493G>A | p.Gly165Ser | missense_variant | 1/1 | ENST00000374519.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RY4 | ENST00000374519.4 | c.493G>A | p.Gly165Ser | missense_variant | 1/1 | NM_002565.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000622 AC: 7AN: 112550Hom.: 0 Cov.: 24 AF XY: 0.0000864 AC XY: 3AN XY: 34710
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183131Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67625
GnomAD4 exome AF: 0.0000155 AC: 17AN: 1098186Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363542
GnomAD4 genome AF: 0.0000622 AC: 7AN: 112550Hom.: 0 Cov.: 24 AF XY: 0.0000864 AC XY: 3AN XY: 34710
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.493G>A (p.G165S) alteration is located in exon 1 (coding exon 1) of the P2RY4 gene. This alteration results from a G to A substitution at nucleotide position 493, causing the glycine (G) at amino acid position 165 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