chr17-82616012-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_019613.4(WDR45B):c.942C>T(p.Asp314Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00741 in 1,613,774 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0059 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0076 ( 65 hom. )

Consequence

WDR45B
NM_019613.4 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.868

Variant links:

Genes affected

WDR45B (HGNC:25072): (WD repeat domain 45B) This gene encodes a member of the WIPI or SVP1 family of WD40 repeat-containing proteins. The protein contains seven WD40 repeats that are thought to fold into a beta-propeller structure that mediates protein-protein interactions, and a conserved motif for interaction with phospholipids. The human genome contains several pseudogenes of this gene. [provided by RefSeq, Jul 2008]

WDR45B links:

FOXK2 (HGNC:6036): (forkhead box K2) The protein encoded by this gene contains a fork head DNA binding domain. This protein can bind to the purine-rich motifs of the HIV long terminal repeat (LTR), and to the similar purine-rich motif in the interleukin 2 (IL2) promoter. It may be involved in the regulation of viral and cellular promoter elements. [provided by RefSeq, Jul 2008]

FOXK2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 17-82616012-G-A is Benign according to our data. Variant chr17-82616012-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 774726.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.868 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 65 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR45B	NM_019613.4 link	c.942C>T	p.Asp314Asp	synonymous_variant	Exon 10 of 10	ENST00000392325.9	NP_062559.2	Q5MNZ6
WDR45B	XM_005256377.6 link	c.840C>T	p.Asp280Asp	synonymous_variant	Exon 9 of 9		XP_005256434.1
WDR45B	XM_047436412.1 link	c.786C>T	p.Asp262Asp	synonymous_variant	Exon 8 of 8		XP_047292368.1
WDR45B	XM_047436413.1 link	c.588C>T	p.Asp196Asp	synonymous_variant	Exon 10 of 10		XP_047292369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR45B	ENST00000392325.9 link	c.942C>T	p.Asp314Asp	synonymous_variant	Exon 10 of 10	1	NM_019613.4	ENSP00000376139.4		Q5MNZ6

Frequencies

GnomAD3 genomes

AF:

0.00591

AC:

899

AN:

152040

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00193

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.00663

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00557

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00912

Gnomad OTH

AF:

0.00431

GnomAD2 exomes

AF:

0.00572

AC:

1436

AN:

251154

AF XY:

0.00583

show subpopulations

Gnomad AFR exome

AF:

0.00222

Gnomad AMR exome

AF:

0.00483

Gnomad ASJ exome

AF:

0.00308

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00497

Gnomad NFE exome

AF:

0.00877

Gnomad OTH exome

AF:

0.00603

GnomAD4 exome

AF:

0.00757

AC:

11061

AN:

1461618

Hom.:

Cov.:

AF XY:

0.00728

AC XY:

5297

AN XY:

727130

show subpopulations

African (AFR)

AF:

0.00185

AC:

AN:

33476

American (AMR)

AF:

0.00519

AC:

232

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00390

AC:

102

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00165

AC:

142

AN:

86258

European-Finnish (FIN)

AF:

0.00502

AC:

268

AN:

53336

Middle Eastern (MID)

AF:

0.00173

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00883

AC:

9818

AN:

1111830

Other (OTH)

AF:

0.00707

AC:

427

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.448

Heterozygous variant carriers

526

1052

1577

2103

2629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00591

AC:

899

AN:

152156

Hom.:

Cov.:

AF XY:

0.00554

AC XY:

412

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.00193

AC:

AN:

41512

American (AMR)

AF:

0.00662

AC:

101

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.00403

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.00145

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.00557

AC:

AN:

10596

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00912

AC:

620

AN:

68002

Other (OTH)

AF:

0.00427

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

136

181

226

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00717

Hom.:

Bravo

AF:

0.00568

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00905

EpiControl

AF:

0.00984

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Apr 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

WDR45B: BP4, BP7, BS2 -

Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures

Benign:1

Sep 27, 2021

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

7.4

(source)

DANN

Benign

0.82

PhyloP100

0.87

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

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chr17-82616012-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over