rs778602062
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002641.4(PIGA):c.981+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,194,617 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 110 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002641.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGA | NM_002641.4 | c.981+8G>A | splice_region_variant, intron_variant | ENST00000333590.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGA | ENST00000333590.6 | c.981+8G>A | splice_region_variant, intron_variant | 1 | NM_002641.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000625 AC: 7AN: 112055Hom.: 0 Cov.: 23 AF XY: 0.000175 AC XY: 6AN XY: 34231
GnomAD3 exomes AF: 0.000308 AC: 51AN: 165842Hom.: 0 AF XY: 0.000526 AC XY: 29AN XY: 55182
GnomAD4 exome AF: 0.000188 AC: 203AN: 1082562Hom.: 0 Cov.: 29 AF XY: 0.000294 AC XY: 104AN XY: 353772
GnomAD4 genome ? AF: 0.0000625 AC: 7AN: 112055Hom.: 0 Cov.: 23 AF XY: 0.000175 AC XY: 6AN XY: 34231
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | PIGA: BP4, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Multiple congenital anomalies-hypotonia-seizures syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2023 | - - |
PIGA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 27, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at