15-43827995-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024908.4(WDR76):c.91G>T(p.Ala31Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,607,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024908.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR76 | NM_024908.4 | c.91G>T | p.Ala31Ser | missense_variant | 2/13 | ENST00000263795.11 | NP_079184.2 | |
WDR76 | NM_001167941.2 | c.-22-80G>T | intron_variant | NP_001161413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR76 | ENST00000263795.11 | c.91G>T | p.Ala31Ser | missense_variant | 2/13 | 1 | NM_024908.4 | ENSP00000263795.6 | ||
WDR76 | ENST00000381246.6 | c.-102G>T | 5_prime_UTR_variant | 2/13 | 1 | ENSP00000370645.2 | ||||
WDR76 | ENST00000452115.1 | c.-22-80G>T | intron_variant | 5 | ENSP00000404665.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000368 AC: 9AN: 244510Hom.: 0 AF XY: 0.0000455 AC XY: 6AN XY: 131976
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1455452Hom.: 0 Cov.: 29 AF XY: 0.0000290 AC XY: 21AN XY: 723686
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2024 | The c.91G>T (p.A31S) alteration is located in exon 2 (coding exon 2) of the WDR76 gene. This alteration results from a G to T substitution at nucleotide position 91, causing the alanine (A) at amino acid position 31 to be replaced by a serine (S). 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