chr15-55340648-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004855.5(PIGB):c.883G>A(p.Val295Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000484 in 1,612,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V295V) has been classified as Likely benign.
Frequency
Consequence
NM_004855.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGB | NM_004855.5 | c.883G>A | p.Val295Met | missense_variant | 8/12 | ENST00000164305.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGB | ENST00000164305.10 | c.883G>A | p.Val295Met | missense_variant | 8/12 | 1 | NM_004855.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151904Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247104Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 134012
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1460338Hom.: 0 Cov.: 29 AF XY: 0.0000578 AC XY: 42AN XY: 726298
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151904Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74148
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2022 | This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 295 of the PIGB protein (p.Val295Met). This variant is present in population databases (rs749091489, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with PIGB-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at