17-82648296-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_019613.4(WDR45B):c.45C>T(p.Tyr15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000933 in 1,606,894 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 0.000020 ( 0 hom., cov: 28)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
WDR45B
NM_019613.4 synonymous
NM_019613.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 0.594
Genes affected
WDR45B (HGNC:25072): (WD repeat domain 45B) This gene encodes a member of the WIPI or SVP1 family of WD40 repeat-containing proteins. The protein contains seven WD40 repeats that are thought to fold into a beta-propeller structure that mediates protein-protein interactions, and a conserved motif for interaction with phospholipids. The human genome contains several pseudogenes of this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 17-82648296-G-A is Benign according to our data. Variant chr17-82648296-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 725326.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.594 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR45B | NM_019613.4 | c.45C>T | p.Tyr15= | synonymous_variant | 1/10 | ENST00000392325.9 | |
WDR45B | XM_005256377.6 | c.45C>T | p.Tyr15= | synonymous_variant | 1/9 | ||
WDR45B | XM_047436414.1 | c.45C>T | p.Tyr15= | synonymous_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR45B | ENST00000392325.9 | c.45C>T | p.Tyr15= | synonymous_variant | 1/10 | 1 | NM_019613.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151718Hom.: 0 Cov.: 28
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GnomAD4 exome AF: 0.00000825 AC: 12AN: 1455176Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 723950
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151718Hom.: 0 Cov.: 28 AF XY: 0.0000270 AC XY: 2AN XY: 74004
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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 | Invitae | May 09, 2018 | - - |
Computational scores
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Name
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Cadd
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at