chr2-19946495-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001006657.2(WDR35):c.1633C>T(p.Arg545Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,468 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001006657.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR35 | NM_001006657.2 | c.1633C>T | p.Arg545Ter | stop_gained | 16/28 | ENST00000345530.8 | |
WDR35 | NM_020779.4 | c.1600C>T | p.Arg534Ter | stop_gained | 15/27 | ENST00000281405.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR35 | ENST00000345530.8 | c.1633C>T | p.Arg545Ter | stop_gained | 16/28 | 1 | NM_001006657.2 | A1 | |
WDR35 | ENST00000281405.9 | c.1600C>T | p.Arg534Ter | stop_gained | 15/27 | 1 | NM_020779.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251334Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135826
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461344Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727000
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
Short-rib thoracic dysplasia 7 with or without polydactyly Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 08, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at