rs145602990
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004204.5(PIGQ):c.1505G>A(p.Arg502Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,610,404 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004204.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00103 AC: 257AN: 250566Hom.: 2 AF XY: 0.00115 AC XY: 156AN XY: 135646
GnomAD4 exome AF: 0.00141 AC: 2062AN: 1458038Hom.: 4 Cov.: 29 AF XY: 0.00143 AC XY: 1040AN XY: 725572
GnomAD4 genome AF: 0.000735 AC: 112AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:2
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PIGQ: BP4 -
PIGQ-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Epilepsy Benign:1
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Developmental and epileptic encephalopathy, 77 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at