Variant X-118404440-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_019045.5(WDR44):c.1377T>A(p.Asp459Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,166,101 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000018 ( 0 hom., 1 hem., cov: 23)

Exomes 𝑓: 0.000018 ( 0 hom. 7 hem. )

Consequence

WDR44
NM_019045.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.335

Variant links:

Genes affected

WDR44 (HGNC:30512): (WD repeat domain 44) This gene encodes a protein that interacts with the small GTPase rab11. A similar protein in rat binds the GTP-containing active form of rab11. This protein may play a role in endosome recycling. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

WDR44 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.19215328).

BS2

High Hemizygotes in GnomAdExome4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR44	NM_019045.5 linkuse as main transcript	c.1377T>A	p.Asp459Glu	missense_variant	9/20	ENST00000254029.8	NP_061918.3	Q5JSH3-1
WDR44	NM_001184965.2 linkuse as main transcript	c.1377T>A	p.Asp459Glu	missense_variant	9/20		NP_001171894.1	Q5JSH3-2
WDR44	NM_001184966.1 linkuse as main transcript	c.1302T>A	p.Asp434Glu	missense_variant	8/18		NP_001171895.1	Q5JSH3-4
WDR44	XM_011531353.4 linkuse as main transcript	c.1302T>A	p.Asp434Glu	missense_variant	8/19		XP_011529655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
WDR44	ENST00000254029.8 linkuse as main transcript	c.1377T>A	p.Asp459Glu	missense_variant	9/20	1	NM_019045.5	ENSP00000254029.3	Q5JSH3-1
WDR44	ENST00000371825.7 linkuse as main transcript	c.1377T>A	p.Asp459Glu	missense_variant	9/20	1		ENSP00000360890.3	Q5JSH3-2
WDR44	ENST00000371848.3 linkuse as main transcript	c.1074T>A	p.Asp358Glu	missense_variant	6/18	1		ENSP00000360914.3	H7BY83
WDR44	ENST00000371822.9 linkuse as main transcript	c.1302T>A	p.Asp434Glu	missense_variant	8/18	2		ENSP00000360887.5	Q5JSH3-4

Frequencies

GnomAD3 genomes

AF:

0.0000178

AC:

AN:

112308

Hom.:

Cov.:

AF XY:

0.0000290

AC XY:

AN XY:

34472

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000375

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000605

AC:

AN:

165241

Hom.:

AF XY:

0.00

AC XY:

AN XY:

53383

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000131

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000180

AC:

AN:

1053793

Hom.:

Cov.:

AF XY:

0.0000217

AC XY:

AN XY:

323279

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000235

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000178

AC:

AN:

112308

Hom.:

Cov.:

AF XY:

0.0000290

AC XY:

AN XY:

34472

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000375

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 05, 2023

The c.1377T>A (p.D459E) alteration is located in exon 9 (coding exon 9) of the WDR44 gene. This alteration results from a T to A substitution at nucleotide position 1377, causing the aspartic acid (D) at amino acid position 459 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.77

BayesDel_addAF

Uncertain

0.075

BayesDel_noAF

Benign

-0.13

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.24

.;T;.

FATHMM_MKL

Uncertain

0.89

LIST_S2

Uncertain

0.92

D;D;D

M_CAP

Benign

0.040

MetaRNN

Benign

0.19

T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.4

.;L;L

PrimateAI

Uncertain

0.68

PROVEAN

Benign

-0.43

N;N;N

REVEL

Benign

0.28

Sift

Benign

0.15

T;T;T

Sift4G

Benign

0.64

T;T;T

Polyphen

0.14, 1.0

.;B;D

Vest4

0.45

MutPred

0.15

.;Gain of ubiquitination at K455 (P = 0.1204);Gain of ubiquitination at K455 (P = 0.1204);

MVP

0.71

MPC

1.1

ClinPred

0.17

GERP RS

-0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.20

gMVP

0.43

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