chr15-89727331-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020212.2(WDR93):c.1052+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,613,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000066 ( 0 hom. )
Consequence
WDR93
NM_020212.2 splice_donor_region, intron
NM_020212.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00002071
2
Clinical Significance
Conservation
PhyloP100: 2.25
Genes affected
WDR93 (HGNC:26924): (WD repeat domain 93) Predicted to enable oxidoreductase activity, acting on NAD(P)H. Predicted to be involved in electron transport chain. Predicted to be part of mitochondrial respiratory chain complex I. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 15-89727331-G-A is Benign according to our data. Variant chr15-89727331-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2645699.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR93 | NM_020212.2 | c.1052+3G>A | splice_donor_region_variant, intron_variant | ENST00000268130.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR93 | ENST00000268130.12 | c.1052+3G>A | splice_donor_region_variant, intron_variant | 1 | NM_020212.2 | P2 | |||
WDR93 | ENST00000560294.5 | c.1052+3G>A | splice_donor_region_variant, intron_variant | 2 | A2 | ||||
WDR93 | ENST00000444934.3 | n.558+3G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
WDR93 | ENST00000557825.5 | n.441+3G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000922 AC: 23AN: 249450Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135140
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GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461116Hom.: 0 Cov.: 30 AF XY: 0.0000922 AC XY: 67AN XY: 726848
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | WDR93: BP4 - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at