15-84643406-G-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032856.5(WDR73):c.*64C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 1,524,954 control chromosomes in the GnomAD database, including 494,972 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.73 ( 41834 hom., cov: 33)
Exomes 𝑓: 0.81 ( 453138 hom. )
Consequence
WDR73
NM_032856.5 3_prime_UTR
NM_032856.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00800
Genes affected
WDR73 (HGNC:25928): (WD repeat domain 73) The protein encoded by this gene is thought to contain multiple WD40 repeats. WD40 repeats are motifs that contain 40-60 amino acids, and usually end with Trp-Asp (WD). This protein is found in the cytoplasm during interphase, but accumulates at the spindle poles and astral microtubules during mitosis. Reduced expression of this gene results in abnormalities in the size and morphology of the nucleus. Mutations in this gene have been associated with Galloway-Mowat syndrome PMID: 25466283), which is a rare autosomal recessive disorder that affects both the central nervous system and kidneys. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 15-84643406-G-C is Benign according to our data. Variant chr15-84643406-G-C is described in ClinVar as [Benign]. Clinvar id is 1256945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-84643406-G-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.733 AC: 111461AN: 152038Hom.: 41831 Cov.: 33
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GnomAD4 exome AF: 0.809 AC: 1111129AN: 1372798Hom.: 453138 Cov.: 31 AF XY: 0.808 AC XY: 544722AN XY: 674252
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GnomAD4 genome AF: 0.733 AC: 111507AN: 152156Hom.: 41834 Cov.: 33 AF XY: 0.727 AC XY: 54088AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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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