chr11-73234457-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002564.4(P2RY2):c.298C>T(p.Pro100Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000102 in 1,614,160 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002564.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
P2RY2 | NM_002564.4 | c.298C>T | p.Pro100Ser | missense_variant | Exon 3 of 3 | ENST00000393597.7 | NP_002555.4 | |
P2RY2 | NM_176071.3 | c.298C>T | p.Pro100Ser | missense_variant | Exon 3 of 3 | NP_788085.3 | ||
P2RY2 | NM_176072.3 | c.298C>T | p.Pro100Ser | missense_variant | Exon 3 of 3 | NP_788086.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P2RY2 | ENST00000393597.7 | c.298C>T | p.Pro100Ser | missense_variant | Exon 3 of 3 | 1 | NM_002564.4 | ENSP00000377222.2 | ||
P2RY2 | ENST00000311131.6 | c.298C>T | p.Pro100Ser | missense_variant | Exon 3 of 3 | 1 | ENSP00000310305.2 | |||
P2RY2 | ENST00000393596.2 | c.298C>T | p.Pro100Ser | missense_variant | Exon 3 of 3 | 1 | ENSP00000377221.2 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152232Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251206Hom.: 1 AF XY: 0.000228 AC XY: 31AN XY: 135782
GnomAD4 exome AF: 0.000103 AC: 151AN: 1461810Hom.: 3 Cov.: 57 AF XY: 0.000155 AC XY: 113AN XY: 727214
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152350Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 8AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.298C>T (p.P100S) alteration is located in exon 3 (coding exon 1) of the P2RY2 gene. This alteration results from a C to T substitution at nucleotide position 298, causing the proline (P) at amino acid position 100 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