X-48601934-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001347217.2(WDR13):c.982G>A(p.Val328Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000753 in 1,194,775 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 281 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., 29 hem., cov: 24)

Exomes 𝑓: 0.00075 ( 0 hom. 252 hem. )

Consequence

WDR13
NM_001347217.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:3

Conservation

PhyloP100: 1.99

Publications

2 publications found

Variant links:

Genes affected

WDR13 (HGNC:14352): (WD repeat domain 13) 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. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. A similar protein in mouse is thought to be a negative regulator of the pancreatic beta cell proliferation. Mice lacking this gene exhibit increased pancreatic islet mass and higher serum insulin levels, and are mildly obese. [provided by RefSeq, Nov 2016]

WDR13 Gene-Disease associations (from GenCC):

intellectual disability
Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics

WDR13 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011793971).

BP6

Variant X-48601934-G-A is Benign according to our data. Variant chrX-48601934-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 715468.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 29 XL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001347217.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
WDR13	NM_001347217.2	MANE Select	c.982G>A	p.Val328Ile	missense	Exon 7 of 10	NP_001334146.1	Q9H1Z4-1
WDR13	NM_017883.6		c.982G>A	p.Val328Ile	missense	Exon 6 of 9	NP_060353.2
WDR13	NM_001166426.3		c.706G>A	p.Val236Ile	missense	Exon 5 of 8	NP_001159898.1	Q9H1Z4-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
WDR13	ENST00000376729.10	TSL:5 MANE Select	c.982G>A	p.Val328Ile	missense	Exon 7 of 10	ENSP00000365919.5	Q9H1Z4-1
WDR13	ENST00000218056.9	TSL:1	c.982G>A	p.Val328Ile	missense	Exon 6 of 9	ENSP00000218056.5	Q9H1Z4-1
WDR13	ENST00000479279.5	TSL:1	n.1849G>A		non_coding_transcript_exon	Exon 5 of 8

Frequencies

GnomAD3 genomes

AF:

0.000798

AC:

AN:

112719

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00112

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000361

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00837

Gnomad NFE

AF:

0.00135

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000674

AC:

114

AN:

169097

AF XY:

0.000675

show subpopulations

Gnomad AFR exome

AF:

0.0000767

Gnomad AMR exome

AF:

0.00105

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00106

Gnomad OTH exome

AF:

0.000729

GnomAD4 exome

AF:

0.000750

AC:

811

AN:

1082003

Hom.:

Cov.:

AF XY:

0.000718

AC XY:

252

AN XY:

350859

show subpopulations

African (AFR)

AF:

0.000115

AC:

AN:

26154

American (AMR)

AF:

0.00106

AC:

AN:

33991

Ashkenazi Jewish (ASJ)

AF:

0.0000544

AC:

AN:

18391

East Asian (EAS)

AF:

0.00

AC:

AN:

29973

South Asian (SAS)

AF:

0.000503

AC:

AN:

51697

European-Finnish (FIN)

AF:

0.0000250

AC:

AN:

40029

Middle Eastern (MID)

AF:

0.00123

AC:

AN:

4055

European-Non Finnish (NFE)

AF:

0.000849

AC:

707

AN:

832378

Other (OTH)

AF:

0.000706

AC:

AN:

45335

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

108

144

180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000789

AC:

AN:

112772

Hom.:

Cov.:

AF XY:

0.000830

AC XY:

AN XY:

34924

show subpopulations

African (AFR)

AF:

0.0000962

AC:

AN:

31170

American (AMR)

AF:

0.00112

AC:

AN:

10686

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2654

East Asian (EAS)

AF:

0.00

AC:

AN:

3592

South Asian (SAS)

AF:

0.00

AC:

AN:

2763

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6220

Middle Eastern (MID)

AF:

0.00917

AC:

AN:

218

European-Non Finnish (NFE)

AF:

0.00135

AC:

AN:

53244

Other (OTH)

AF:

0.00

AC:

AN:

1540

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00129

Hom.:

Bravo

AF:

0.000774

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00149

AC:

ExAC

AF:

0.000528

AC:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.64

CADD

Benign

8.6

(source)

DANN

Benign

0.26

DEOGEN2

Benign

0.013

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.81

M_CAP

Benign

0.017

MetaRNN

Benign

0.012

MetaSVM

Benign

-1.0

PhyloP100

2.0

PrimateAI

Uncertain

0.49

PROVEAN

Benign

0.64

REVEL

Benign

0.066

Sift

Benign

1.0

Sift4G

Benign

1.0

Vest4

0.084

MVP

0.12

MPC

0.83

ClinPred

0.0049

GERP RS

3.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

gMVP

0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over