Variant 3-49015786-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018031.6(WDR6):c.*498A>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 0.795 in 1,613,944 control chromosomes in the GnomAD database, including 513,796 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.82 ( 51501 hom., cov: 31)

Exomes 𝑓: 0.79 ( 462295 hom. )

Consequence

WDR6
NM_018031.6 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.99

Variant links:

Genes affected

WDR6 (HGNC:12758): (WD repeat domain 6) 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), which may facilitate formation of heterotrimeric or multiprotein complexes. The encoded protein interacts with serine/threonine kinase 11, and is implicated in cell growth arrest. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]

WDR6 links:

DALRD3 (HGNC:25536): (DALR anticodon binding domain containing 3) The exact function of this gene is not known. It encodes a protein with a DALR anticodon binding domain similar to that of class Ia aminoacyl tRNA synthetases. This gene is located in a cluster of genes (with a complex sense-anti-sense genome architecture) on chromosome 3, and contains two micro RNA (miRNA) precursors (mir-425 and mir-191) in one of its introns. Preferential expression of this gene (the miRNAs and other genes in the cluster) in testis suggests a role of this gene in spermatogenesis (PMID:19906709). [provided by RefSeq, Feb 2013]

DALRD3 links:

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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=-0.85).

BP6

Variant 3-49015786-A-G is Benign according to our data. Variant chr3-49015786-A-G is described in ClinVar as [Benign]. Clinvar id is 1342120.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR6	NM_018031.6 link	c.*498A>G		3_prime_UTR_variant	6/6	ENST00000608424.6	NP_060501.4	Q9NNW5A0A087X295Q9H9M3B3KRR8
DALRD3	NM_001009996.3 link	c.1512+18T>C		intron_variant		ENST00000341949.9	NP_001009996.1	Q5D0E6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR6	ENST00000608424.6 link	c.*498A>G		3_prime_UTR_variant	6/6	1	NM_018031.6	ENSP00000477389.1		Q9NNW5
DALRD3	ENST00000341949.9 link	c.1512+18T>C		intron_variant		1	NM_001009996.3	ENSP00000344989.4		Q5D0E6-1

Frequencies

GnomAD3 genomes

AF:

0.820

AC:

124625

AN:

151966

Hom.:

51453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.883

Gnomad AMI

AF:

0.732

Gnomad AMR

AF:

0.847

Gnomad ASJ

AF:

0.873

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.942

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.754

Gnomad OTH

AF:

0.806

GnomAD3 exomes

AF:

0.833

AC:

209501

AN:

251398

Hom.:

88354

AF XY:

0.832

AC XY:

113030

AN XY:

135864

show subpopulations

Gnomad AFR exome

AF:

0.882

Gnomad AMR exome

AF:

0.901

Gnomad ASJ exome

AF:

0.873

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.939

Gnomad FIN exome

AF:

0.805

Gnomad NFE exome

AF:

0.754

Gnomad OTH exome

AF:

0.808

GnomAD4 exome

AF:

0.793

AC:

1158581

AN:

1461860

Hom.:

462295

Cov.:

AF XY:

0.796

AC XY:

578778

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.886

Gnomad4 AMR exome

AF:

0.895

Gnomad4 ASJ exome

AF:

0.872

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.937

Gnomad4 FIN exome

AF:

0.793

Gnomad4 NFE exome

AF:

0.764

Gnomad4 OTH exome

AF:

0.812

GnomAD4 genome

AF:

0.820

AC:

124733

AN:

152084

Hom.:

51501

Cov.:

AF XY:

0.827

AC XY:

61448

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.883

Gnomad4 AMR

AF:

0.848

Gnomad4 ASJ

AF:

0.873

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.942

Gnomad4 FIN

AF:

0.809

Gnomad4 NFE

AF:

0.754

Gnomad4 OTH

AF:

0.809

Alfa

AF:

0.779

Hom.:

63258

Bravo

AF:

0.826

Asia WGS

AF:

0.965

AC:

3356

AN:

3478

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 20, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.034

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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