rs375371562
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002641.4(PIGA):c.716-10A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,080,375 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 38 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002641.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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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.716-10A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000333590.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGA | ENST00000333590.6 | c.716-10A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002641.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 17AN: 112322Hom.: 0 Cov.: 23 AF XY: 0.000174 AC XY: 6AN XY: 34464
GnomAD3 exomes AF: 0.000107 AC: 16AN: 148852Hom.: 0 AF XY: 0.000112 AC XY: 5AN XY: 44824
GnomAD4 exome AF: 0.000118 AC: 114AN: 968053Hom.: 0 Cov.: 16 AF XY: 0.000120 AC XY: 32AN XY: 266087
GnomAD4 genome ? AF: 0.000151 AC: 17AN: 112322Hom.: 0 Cov.: 23 AF XY: 0.000174 AC XY: 6AN XY: 34464
ClinVar
Submissions by phenotype
Multiple congenital anomalies-hypotonia-seizures syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at