rs3745032
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_015285.3(WDR7):c.*112C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 1,336,130 control chromosomes in the GnomAD database, including 501 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.021 ( 37 hom., cov: 32)
Exomes 𝑓: 0.025 ( 464 hom. )
Consequence
WDR7
NM_015285.3 3_prime_UTR
NM_015285.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.62
Genes affected
WDR7 (HGNC:13490): (WD repeat domain 7) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD) that may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. The encoded protein forms the beta subunit of rabconnectin-3 and binds directly with Rab3A GDP/GTP exchange protein and indirectly with Rab3A GDP/GTP activating protein; these proteins are regulators of Rab3 small G protein family members involved in control of the calcium-dependant exocytosis of neurotransmitters. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0208 (3039/145962) while in subpopulation EAS AF= 0.0506 (260/5140). AF 95% confidence interval is 0.0455. There are 37 homozygotes in gnomad4. There are 1427 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3039 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR7 | NM_015285.3 | c.*112C>T | 3_prime_UTR_variant | 28/28 | ENST00000254442.8 | NP_056100.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR7 | ENST00000254442.8 | c.*112C>T | 3_prime_UTR_variant | 28/28 | 1 | NM_015285.3 | ENSP00000254442.3 | |||
WDR7 | ENST00000357574.7 | c.*112C>T | 3_prime_UTR_variant | 27/27 | 5 | ENSP00000350187.2 | ||||
WDR7 | ENST00000589935.1 | c.*112C>T | downstream_gene_variant | 4 | ENSP00000467485.1 |
Frequencies
GnomAD3 genomes AF: 0.0208 AC: 3037AN: 145852Hom.: 37 Cov.: 32
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GnomAD4 exome AF: 0.0254 AC: 30193AN: 1190168Hom.: 464 Cov.: 18 AF XY: 0.0246 AC XY: 14440AN XY: 585964
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GnomAD4 genome AF: 0.0208 AC: 3039AN: 145962Hom.: 37 Cov.: 32 AF XY: 0.0200 AC XY: 1427AN XY: 71474
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at