chr22-21016070-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005446.5(P2RX6):c.293C>A(p.Ala98Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,563,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005446.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P2RX6 | ENST00000413302.7 | c.293C>A | p.Ala98Asp | missense_variant | Exon 2 of 12 | 1 | NM_005446.5 | ENSP00000416193.2 | ||
ENSG00000291240 | ENST00000706202.1 | n.1733-2886G>T | intron_variant | Intron 4 of 6 | ENSP00000516280.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000174 AC: 3AN: 172512Hom.: 0 AF XY: 0.0000328 AC XY: 3AN XY: 91506
GnomAD4 exome AF: 0.0000220 AC: 31AN: 1411216Hom.: 0 Cov.: 31 AF XY: 0.0000229 AC XY: 16AN XY: 697454
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.293C>A (p.A98D) alteration is located in exon 2 (coding exon 2) of the P2RX6 gene. This alteration results from a C to A substitution at nucleotide position 293, causing the alanine (A) at amino acid position 98 to be replaced by an aspartic acid (D). 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