rs1475940439
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001006657.2(WDR35):c.3528C>T(p.Cys1176=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000658 in 152,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
WDR35
NM_001006657.2 synonymous
NM_001006657.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.81
Genes affected
WDR35 (HGNC:29250): (WD repeat domain 35) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Two patients with Sensenbrenner syndrome / cranioectodermal dysplasia (CED) were identified with mutations in this gene, consistent with a possible ciliary function.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| WDR35 | NM_001006657.2 | c.3528C>T | p.Cys1176= | synonymous_variant | 28/28 | ENST00000345530.8 | |
| WDR35 | NM_020779.4 | c.3495C>T | p.Cys1165= | synonymous_variant | 27/27 | ENST00000281405.9 | |
| WDR35 | XM_011533007.3 | c.2223C>T | p.Cys741= | synonymous_variant | 17/17 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| WDR35 | ENST00000345530.8 | c.3528C>T | p.Cys1176= | synonymous_variant | 28/28 | 1 | NM_001006657.2 | A1 | |
| WDR35 | ENST00000281405.9 | c.3495C>T | p.Cys1165= | synonymous_variant | 27/27 | 1 | NM_020779.4 | P3 | |
| WDR35 | ENST00000414212.5 | c.*810C>T | 3_prime_UTR_variant, NMD_transcript_variant | 28/28 | 5 | ||||
| WDR35 | ENST00000445063.5 | c.*1702C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 2 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152026Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 31
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GnomAD4 genome 0.00000658 AC: 1AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74248
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at