rs2567998
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002562.6(P2RX7):c.1189-16A>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00366 in 1,472,950 control chromosomes in the GnomAD database, including 172 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002562.6 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX7 | NM_002562.6 | c.1189-16A>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000328963.10 | |||
LOC105370032 | XR_001749352.3 | n.327+23160T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX7 | ENST00000328963.10 | c.1189-16A>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002562.6 | P1 | |||
ENST00000652651.1 | n.3549-2390T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0189 AC: 2876AN: 152100Hom.: 101 Cov.: 31
GnomAD3 exomes AF: 0.00541 AC: 1183AN: 218478Hom.: 38 AF XY: 0.00408 AC XY: 485AN XY: 118910
GnomAD4 exome AF: 0.00190 AC: 2511AN: 1320734Hom.: 71 Cov.: 18 AF XY: 0.00163 AC XY: 1080AN XY: 662590
GnomAD4 genome AF: 0.0190 AC: 2887AN: 152216Hom.: 101 Cov.: 31 AF XY: 0.0183 AC XY: 1363AN XY: 74414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at