rs116591352
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004278.4(PIGL):c.535G>A(p.Val179Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V179L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004278.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGL | NM_004278.4 | c.535G>A | p.Val179Met | missense_variant | 6/7 | ENST00000225609.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGL | ENST00000225609.10 | c.535G>A | p.Val179Met | missense_variant | 6/7 | 1 | NM_004278.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251464Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135906
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461630Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727124
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74508
ClinVar
Submissions by phenotype
CHIME syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at