rs1191779
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020779.4(WDR35):c.2824-14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 1,612,746 control chromosomes in the GnomAD database, including 795,306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020779.4 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR35 | NM_001006657.2 | c.2857-14G>T | intron_variant | Intron 24 of 27 | ENST00000345530.8 | NP_001006658.1 | ||
WDR35 | NM_020779.4 | c.2824-14G>T | intron_variant | Intron 23 of 26 | ENST00000281405.9 | NP_065830.2 | ||
WDR35 | XM_011533007.3 | c.1552-14G>T | intron_variant | Intron 13 of 16 | XP_011531309.1 | |||
WDR35 | XR_426989.4 | n.2814-14G>T | intron_variant | Intron 23 of 24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR35 | ENST00000345530.8 | c.2857-14G>T | intron_variant | Intron 24 of 27 | 1 | NM_001006657.2 | ENSP00000314444.5 | |||
WDR35 | ENST00000281405.9 | c.2824-14G>T | intron_variant | Intron 23 of 26 | 1 | NM_020779.4 | ENSP00000281405.5 | |||
WDR35 | ENST00000414212.5 | n.*139-14G>T | intron_variant | Intron 24 of 27 | 5 | ENSP00000390802.1 | ||||
WDR35 | ENST00000445063.5 | n.*1272-14G>T | intron_variant | Intron 15 of 17 | 2 | ENSP00000390105.1 |
Frequencies
GnomAD3 genomes AF: 0.970 AC: 147581AN: 152112Hom.: 71734 Cov.: 31
GnomAD3 exomes AF: 0.990 AC: 248082AN: 250652Hom.: 122857 AF XY: 0.991 AC XY: 134376AN XY: 135620
GnomAD4 exome AF: 0.995 AC: 1453574AN: 1460518Hom.: 723524 Cov.: 42 AF XY: 0.995 AC XY: 723044AN XY: 726610
GnomAD4 genome AF: 0.970 AC: 147686AN: 152228Hom.: 71782 Cov.: 31 AF XY: 0.971 AC XY: 72248AN XY: 74430
ClinVar
Submissions by phenotype
not specified Benign:6
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
- -
- -
- -
- -
Cranioectodermal dysplasia 2 Benign:2
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Short-rib thoracic dysplasia 7 with or without polydactyly Benign:2
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Cranioectodermal dysplasia 2;C3279792:Short-rib thoracic dysplasia 7 with or without polydactyly Benign:1
- -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at