rs1106042
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_004764.5(PIWIL1):c.1580G>A(p.Arg527Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0661 in 1,608,668 control chromosomes in the GnomAD database, including 4,817 homozygotes. 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 Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004764.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIWIL1 | NM_004764.5 | c.1580G>A | p.Arg527Lys | missense_variant | 13/21 | ENST00000245255.7 | NP_004755.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIWIL1 | ENST00000245255.7 | c.1580G>A | p.Arg527Lys | missense_variant | 13/21 | 1 | NM_004764.5 | ENSP00000245255.3 |
Frequencies
GnomAD3 genomes AF: 0.0561 AC: 8543AN: 152154Hom.: 367 Cov.: 33
GnomAD3 exomes AF: 0.0740 AC: 18425AN: 249136Hom.: 1026 AF XY: 0.0810 AC XY: 10921AN XY: 134744
GnomAD4 exome AF: 0.0671 AC: 97729AN: 1456396Hom.: 4453 Cov.: 31 AF XY: 0.0712 AC XY: 51552AN XY: 723560
GnomAD4 genome AF: 0.0560 AC: 8529AN: 152272Hom.: 364 Cov.: 33 AF XY: 0.0592 AC XY: 4406AN XY: 74464
ClinVar
Submissions by phenotype
PIWIL1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at