rs710924
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000026218.9(PIGQ):c.2002T>C(p.Cys668Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,611,930 control chromosomes in the GnomAD database, including 166,855 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C668Y) has been classified as Benign.
Frequency
Consequence
ENST00000026218.9 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.*318T>C | 3_prime_UTR_variant | 11/11 | ENST00000321878.10 | ||
PIGQ | NM_148920.4 | c.2002T>C | p.Cys668Arg | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGQ | ENST00000321878.10 | c.*318T>C | 3_prime_UTR_variant | 11/11 | 1 | NM_004204.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.457 AC: 69176AN: 151462Hom.: 16148 Cov.: 33
GnomAD3 exomes AF: 0.488 AC: 121834AN: 249866Hom.: 30899 AF XY: 0.487 AC XY: 66023AN XY: 135492
GnomAD4 exome AF: 0.448 AC: 654291AN: 1460354Hom.: 150678 Cov.: 58 AF XY: 0.452 AC XY: 328380AN XY: 726506
GnomAD4 genome ? AF: 0.457 AC: 69256AN: 151576Hom.: 16177 Cov.: 33 AF XY: 0.465 AC XY: 34447AN XY: 74048
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 72% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 67. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at