4-39257570-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_025132.4(WDR19):c.3183+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,561,466 control chromosomes in the GnomAD database, including 81,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_025132.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR19 | ENST00000399820.8 | c.3183+16A>G | intron_variant | Intron 28 of 36 | 1 | NM_025132.4 | ENSP00000382717.3 | |||
WDR19 | ENST00000506869.5 | n.*2764+16A>G | intron_variant | Intron 27 of 35 | 2 | ENSP00000424319.1 | ||||
WDR19 | ENST00000512095.5 | n.2181+16A>G | intron_variant | Intron 18 of 22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.327 AC: 49636AN: 151930Hom.: 8218 Cov.: 31
GnomAD3 exomes AF: 0.311 AC: 55513AN: 178276Hom.: 8786 AF XY: 0.313 AC XY: 29509AN XY: 94424
GnomAD4 exome AF: 0.319 AC: 450252AN: 1409418Hom.: 73046 Cov.: 30 AF XY: 0.319 AC XY: 222188AN XY: 696168
GnomAD4 genome AF: 0.327 AC: 49658AN: 152048Hom.: 8227 Cov.: 31 AF XY: 0.326 AC XY: 24210AN XY: 74308
ClinVar
Submissions by phenotype
not specified Benign:5
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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. -
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Nephronophthisis 13 Benign:1
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Senior-Loken syndrome 8 Benign:1
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Asphyxiating thoracic dystrophy 5 Benign:1
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not provided Benign:1
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Cranioectodermal dysplasia 4 Benign:1
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Asphyxiating thoracic dystrophy 5;C4225376:Senior-Loken syndrome 8 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at