Variant 15-84643406-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00800

Variant links:

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]

WDR73 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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_single_submitter, 1 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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR73	NM_032856.5 linkuse as main transcript	c.*64C>G		3_prime_UTR_variant	8/8	ENST00000434634.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR73	ENST00000434634.7 linkuse as main transcript	c.*64C>G		3_prime_UTR_variant	8/8	1	NM_032856.5	P1
	ENST00000348993.9 linkuse as main transcript	n.4903G>C		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes

AF:

0.733

AC:

111461

AN:

152038

Hom.:

41831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.587

Gnomad AMI

AF:

0.860

Gnomad AMR

AF:

0.677

Gnomad ASJ

AF:

0.820

Gnomad EAS

AF:

0.580

Gnomad SAS

AF:

0.701

Gnomad FIN

AF:

0.796

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.833

Gnomad OTH

AF:

0.733

GnomAD4 exome

AF:

0.809

AC:

1111129

AN:

1372798

Hom.:

453138

Cov.:

AF XY:

0.808

AC XY:

544722

AN XY:

674252

show subpopulations

Gnomad4 AFR exome

AF:

0.576

Gnomad4 AMR exome

AF:

0.632

Gnomad4 ASJ exome

AF:

0.830

Gnomad4 EAS exome

AF:

0.626

Gnomad4 SAS exome

AF:

0.716

Gnomad4 FIN exome

AF:

0.809

Gnomad4 NFE exome

AF:

0.836

Gnomad4 OTH exome

AF:

0.785

GnomAD4 genome

AF:

0.733

AC:

111507

AN:

152156

Hom.:

41834

Cov.:

AF XY:

0.727

AC XY:

54088

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.587

Gnomad4 AMR

AF:

0.676

Gnomad4 ASJ

AF:

0.820

Gnomad4 EAS

AF:

0.580

Gnomad4 SAS

AF:

0.700

Gnomad4 FIN

AF:

0.796

Gnomad4 NFE

AF:

0.833

Gnomad4 OTH

AF:

0.734

Alfa

AF:

0.780

Hom.:

5819

Bravo

AF:

0.717

Asia WGS

AF:

0.639

AC:

2222

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over