19-12668409-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016145.4(WDR83OS):c.271G>A(p.Val91Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000992 in 1,613,496 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016145.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR83OS | NM_016145.4 | c.271G>A | p.Val91Met | missense_variant | Exon 4 of 4 | ENST00000596731.7 | NP_057229.1 | |
WDR83 | NM_001099737.3 | c.-156-99C>T | intron_variant | Intron 1 of 10 | ENST00000418543.8 | NP_001093207.1 | ||
WDR83 | NR_029375.2 | n.187-99C>T | intron_variant | Intron 1 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR83OS | ENST00000596731.7 | c.271G>A | p.Val91Met | missense_variant | Exon 4 of 4 | 1 | NM_016145.4 | ENSP00000468969.1 | ||
WDR83 | ENST00000418543.8 | c.-156-99C>T | intron_variant | Intron 1 of 10 | 1 | NM_001099737.3 | ENSP00000402653.3 | |||
ENSG00000269590 | ENST00000597961.1 | c.150+719G>A | intron_variant | Intron 2 of 4 | 4 | ENSP00000472710.1 | ||||
ENSG00000285589 | ENST00000648033.1 | n.*4205G>A | non_coding_transcript_exon_variant | Exon 14 of 14 | ENSP00000498000.1 | |||||
ENSG00000285589 | ENST00000648033.1 | n.*4205G>A | 3_prime_UTR_variant | Exon 14 of 14 | ENSP00000498000.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249802Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134988
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461344Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726904
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 91 of the WDR83OS protein (p.Val91Met). This variant is present in population databases (rs368657914, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with WDR83OS-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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