rs144335584
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The ENST00000399820.8(WDR19):āc.2239A>Gā(p.Ile747Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000375 in 1,608,064 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
ENST00000399820.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR19 | NM_025132.4 | c.2239A>G | p.Ile747Val | missense_variant | 19/37 | ENST00000399820.8 | NP_079408.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR19 | ENST00000399820.8 | c.2239A>G | p.Ile747Val | missense_variant | 19/37 | 1 | NM_025132.4 | ENSP00000382717 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000461 AC: 70AN: 151946Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000766 AC: 186AN: 242894Hom.: 0 AF XY: 0.000759 AC XY: 100AN XY: 131720
GnomAD4 exome AF: 0.000367 AC: 534AN: 1456002Hom.: 1 Cov.: 31 AF XY: 0.000398 AC XY: 288AN XY: 724028
GnomAD4 genome AF: 0.000454 AC: 69AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.000525 AC XY: 39AN XY: 74308
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 5 Benign:1
Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Cranioectodermal dysplasia 4 Benign:1
Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Asphyxiating thoracic dystrophy 5;C4225376:Senior-Loken syndrome 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at