rs8176804
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_002583.4(PAWR):c.125C>T(p.Pro42Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000815 in 1,486,592 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002583.4 missense
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 |
---|---|---|---|---|---|---|---|
PAWR | NM_002583.4 | c.125C>T | p.Pro42Leu | missense_variant | 2/7 | ENST00000328827.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAWR | ENST00000328827.9 | c.125C>T | p.Pro42Leu | missense_variant | 2/7 | 1 | NM_002583.4 | P1 | |
PPP1R12A-AS2 | ENST00000551995.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00444 AC: 672AN: 151432Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.000561 AC: 51AN: 90954Hom.: 0 AF XY: 0.000501 AC XY: 26AN XY: 51860
GnomAD4 exome AF: 0.000402 AC: 537AN: 1335048Hom.: 2 Cov.: 30 AF XY: 0.000328 AC XY: 216AN XY: 659090
GnomAD4 genome AF: 0.00445 AC: 674AN: 151544Hom.: 6 Cov.: 31 AF XY: 0.00462 AC XY: 342AN XY: 74058
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at