rs145216283
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004204.5(PIGQ):āc.925C>Gā(p.Leu309Val) variant causes a missense change. The variant allele was found at a frequency of 0.00183 in 1,554,050 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L309L) has been classified 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGQ | NM_004204.5 | c.925C>G | p.Leu309Val | missense_variant | 4/11 | ENST00000321878.10 | |
PIGQ | NM_148920.4 | c.925C>G | p.Leu309Val | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGQ | ENST00000321878.10 | c.925C>G | p.Leu309Val | missense_variant | 4/11 | 1 | NM_004204.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000992 AC: 151AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00109 AC: 172AN: 157760Hom.: 1 AF XY: 0.00111 AC XY: 93AN XY: 83504
GnomAD4 exome AF: 0.00192 AC: 2686AN: 1401684Hom.: 3 Cov.: 34 AF XY: 0.00183 AC XY: 1268AN XY: 691786
GnomAD4 genome ? AF: 0.000991 AC: 151AN: 152366Hom.: 0 Cov.: 34 AF XY: 0.000953 AC XY: 71AN XY: 74498
ClinVar
Submissions by phenotype
PIGQ-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2022 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | PIGQ: BP4 - |
Epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at