14-100468021-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001161476.3(WDR25):c.823G>T(p.Val275Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,520 control chromosomes in the GnomAD database, with no homozygous occurrence. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001161476.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR25 | NM_001161476.3 | c.823G>T | p.Val275Leu | missense_variant, splice_region_variant | 3/7 | ENST00000402312.8 | NP_001154948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR25 | ENST00000402312.8 | c.823G>T | p.Val275Leu | missense_variant, splice_region_variant | 3/7 | 2 | NM_001161476.3 | ENSP00000385540 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249566Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135082
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460396Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726548
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.823G>T (p.V275L) alteration is located in exon 3 (coding exon 2) of the WDR25 gene. This alteration results from a G to T substitution at nucleotide position 823, causing the valine (V) at amino acid position 275 to be replaced by a leucine (L). 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