chr2-19931423-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001006657.2(WDR35):c.2857-14G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Consequence
WDR35
NM_001006657.2 splice_polypyrimidine_tract, intron
NM_001006657.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.09
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR35 | NM_001006657.2 | c.2857-14G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000345530.8 | NP_001006658.1 | |||
WDR35 | NM_020779.4 | c.2824-14G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000281405.9 | NP_065830.2 | |||
WDR35 | XM_011533007.3 | c.1552-14G>C | splice_polypyrimidine_tract_variant, intron_variant | XP_011531309.1 | ||||
WDR35 | XR_426989.4 | n.2814-14G>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR35 | ENST00000281405.9 | c.2824-14G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020779.4 | ENSP00000281405 | P3 | |||
WDR35 | ENST00000345530.8 | c.2857-14G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001006657.2 | ENSP00000314444 | A1 | |||
WDR35 | ENST00000414212.5 | c.*139-14G>C | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 | ENSP00000390802 | |||||
WDR35 | ENST00000445063.5 | c.*1272-14G>C | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 | ENSP00000390105 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 42
GnomAD4 exome
Cov.:
42
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at