chr16-74888296-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030581.4(WDR59):c.2219G>A(p.Arg740Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000109 in 1,613,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R740W) has been classified as Uncertain significance.
Frequency
Consequence
NM_030581.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR59 | NM_030581.4 | c.2219G>A | p.Arg740Gln | missense_variant | 22/26 | ENST00000262144.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR59 | ENST00000262144.11 | c.2219G>A | p.Arg740Gln | missense_variant | 22/26 | 5 | NM_030581.4 | P1 | |
WDR59 | ENST00000563797.5 | c.291-541G>A | intron_variant | 3 | |||||
WDR59 | ENST00000567018.5 | n.481G>A | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
WDR59 | ENST00000569788.5 | n.753G>A | non_coding_transcript_exon_variant | 5/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152016Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000196 AC: 49AN: 250426Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135318
GnomAD4 exome AF: 0.000116 AC: 170AN: 1461420Hom.: 0 Cov.: 34 AF XY: 0.000150 AC XY: 109AN XY: 726970
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.2219G>A (p.R740Q) alteration is located in exon 22 (coding exon 22) of the WDR59 gene. This alteration results from a G to A substitution at nucleotide position 2219, causing the arginine (R) at amino acid position 740 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at