chrX-15331406-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002641.4(PIGA):āc.525T>Cā(p.Leu175Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000542 in 1,209,482 control chromosomes in the GnomAD database, including 6 homozygotes. There are 210 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_002641.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGA | NM_002641.4 | c.525T>C | p.Leu175Leu | synonymous_variant | Exon 2 of 6 | ENST00000333590.6 | NP_002632.1 | |
PIGA | NM_020473.3 | c.13+4095T>C | intron_variant | Intron 1 of 4 | NP_065206.3 | |||
PIGA | NR_033835.1 | n.457+184T>C | intron_variant | Intron 2 of 5 | ||||
PIGA | NR_033836.1 | n.173+468T>C | intron_variant | Intron 2 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000356 AC: 40AN: 112305Hom.: 0 Cov.: 24 AF XY: 0.000464 AC XY: 16AN XY: 34467
GnomAD3 exomes AF: 0.00100 AC: 184AN: 183454Hom.: 1 AF XY: 0.000869 AC XY: 59AN XY: 67894
GnomAD4 exome AF: 0.000561 AC: 615AN: 1097122Hom.: 6 Cov.: 29 AF XY: 0.000535 AC XY: 194AN XY: 362486
GnomAD4 genome AF: 0.000356 AC: 40AN: 112360Hom.: 0 Cov.: 24 AF XY: 0.000463 AC XY: 16AN XY: 34532
ClinVar
Submissions by phenotype
not specified Benign:1
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
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Multiple congenital anomalies-hypotonia-seizures syndrome 2;C3806670:Paroxysmal nocturnal hemoglobinuria 1;CN307964:Neurodevelopmental disorder with epilepsy and hemochromatosis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at