19-12669353-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_016145.4(WDR83OS):c.50+1G>T variant causes a splice donor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_016145.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR83 | NM_001099737.3 | c.-36-402C>A | intron_variant | Intron 2 of 10 | ENST00000418543.8 | NP_001093207.1 | ||
WDR83OS | NM_016145.4 | c.50+1G>T | splice_donor_variant, intron_variant | Intron 1 of 3 | ENST00000596731.7 | NP_057229.1 | ||
WDR83 | NR_029375.2 | n.307-402C>A | intron_variant | Intron 2 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR83 | ENST00000418543.8 | c.-36-402C>A | intron_variant | Intron 2 of 10 | 1 | NM_001099737.3 | ENSP00000402653.3 | |||
WDR83OS | ENST00000596731.7 | c.50+1G>T | splice_donor_variant, intron_variant | Intron 1 of 3 | 1 | NM_016145.4 | ENSP00000468969.1 | |||
ENSG00000269590 | ENST00000597961.1 | c.44+1G>T | splice_donor_variant, intron_variant | Intron 1 of 4 | 4 | ENSP00000472710.1 | ||||
ENSG00000285589 | ENST00000648033.1 | n.*3984+1G>T | splice_donor_variant, intron_variant | Intron 11 of 13 | ENSP00000498000.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hypercholanemia, familial Pathogenic:1
This variant was identified as homozygous in one Turkish individual with neurodevelopmental delay. The variant is absent in gnomAD. In vivo studies in zebrafish suggest wdr83os loss of function is responsible for the human phenotype observed. Other variants in this gene were identified in association with neurodevelopmental delay and hypercholanemia, although bile salt measurements were not available for this patient/variant. -
Neurodevelopmental disorder with variable familial hypercholanemia Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.