chr15-89727279-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020212.2(WDR93):c.1003G>A(p.Ala335Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020212.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR93 | NM_020212.2 | c.1003G>A | p.Ala335Thr | missense_variant | 9/17 | ENST00000268130.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR93 | ENST00000268130.12 | c.1003G>A | p.Ala335Thr | missense_variant | 9/17 | 1 | NM_020212.2 | P2 | |
WDR93 | ENST00000560294.5 | c.1003G>A | p.Ala335Thr | missense_variant | 9/17 | 2 | A2 | ||
WDR93 | ENST00000444934.3 | n.509G>A | non_coding_transcript_exon_variant | 3/11 | 2 | ||||
WDR93 | ENST00000557825.5 | n.392G>A | non_coding_transcript_exon_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251206Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135762
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461828Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 727214
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.1003G>A (p.A335T) alteration is located in exon 9 (coding exon 8) of the WDR93 gene. This alteration results from a G to A substitution at nucleotide position 1003, causing the alanine (A) at amino acid position 335 to be replaced by a threonine (T). 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