rs144493712
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001006657.2(WDR35):āc.2182A>Gā(p.Ile728Val) variant causes a missense change. The variant allele was found at a frequency of 0.00113 in 1,614,166 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I728L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001006657.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR35 | NM_001006657.2 | c.2182A>G | p.Ile728Val | missense_variant | 20/28 | ENST00000345530.8 | |
WDR35 | NM_020779.4 | c.2149A>G | p.Ile717Val | missense_variant | 19/27 | ENST00000281405.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR35 | ENST00000345530.8 | c.2182A>G | p.Ile728Val | missense_variant | 20/28 | 1 | NM_001006657.2 | A1 | |
WDR35 | ENST00000281405.9 | c.2149A>G | p.Ile717Val | missense_variant | 19/27 | 1 | NM_020779.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00291 AC: 443AN: 152198Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00471 AC: 1184AN: 251302Hom.: 24 AF XY: 0.00349 AC XY: 474AN XY: 135808
GnomAD4 exome AF: 0.000944 AC: 1380AN: 1461850Hom.: 24 Cov.: 31 AF XY: 0.000778 AC XY: 566AN XY: 727224
GnomAD4 genome AF: 0.00291 AC: 443AN: 152316Hom.: 8 Cov.: 32 AF XY: 0.00369 AC XY: 275AN XY: 74488
ClinVar
Submissions by phenotype
Cranioectodermal dysplasia 2;C3279792:Short-rib thoracic dysplasia 7 with or without polydactyly Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 18, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 06, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 27, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 11, 2015 | - - |
WDR35-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 14, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cranioectodermal dysplasia 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at