3-39091638-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_020839.4(WDR48):āc.1682A>Gā(p.Lys561Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000522 in 1,605,432 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_020839.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR48 | NM_020839.4 | c.1682A>G | p.Lys561Arg | missense_variant | Exon 17 of 19 | ENST00000302313.10 | NP_065890.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152156Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 255AN: 241856Hom.: 7 AF XY: 0.000948 AC XY: 124AN XY: 130764
GnomAD4 exome AF: 0.000520 AC: 755AN: 1453276Hom.: 10 Cov.: 30 AF XY: 0.000505 AC XY: 365AN XY: 722658
GnomAD4 genome AF: 0.000545 AC: 83AN: 152156Hom.: 1 Cov.: 32 AF XY: 0.000552 AC XY: 41AN XY: 74334
ClinVar
Submissions by phenotype
WDR48-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at