Variant rs10521584 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_019045.5(WDR44):c.1776C>T(p.Asn592=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,208,610 control chromosomes in the GnomAD database, including 8,178 homozygotes. There are 52,006 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 796 hom., 4384 hem., cov: 23)

Exomes 𝑓: 0.13 ( 7382 hom. 47622 hem. )

Consequence

WDR44
NM_019045.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.274

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant X-118432819-C-T is Benign according to our data. Variant chrX-118432819-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.274 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
WDR44	NM_019045.5 linkuse as main transcript	c.1776C>T	p.Asn592=	synonymous_variant	13/20	ENST00000254029.8	NP_061918.3
WDR44	NM_001184965.2 linkuse as main transcript	c.1776C>T	p.Asn592=	synonymous_variant	13/20		NP_001171894.1
WDR44	NM_001184966.1 linkuse as main transcript	c.1701C>T	p.Asn567=	synonymous_variant	12/18		NP_001171895.1
WDR44	XM_011531353.4 linkuse as main transcript	c.1701C>T	p.Asn567=	synonymous_variant	12/19		XP_011529655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR44	ENST00000254029.8 linkuse as main transcript	c.1776C>T	p.Asn592=	synonymous_variant	13/20	1	NM_019045.5	ENSP00000254029	P1	Q5JSH3-1
WDR44	ENST00000371825.7 linkuse as main transcript	c.1776C>T	p.Asn592=	synonymous_variant	13/20	1		ENSP00000360890		Q5JSH3-2
WDR44	ENST00000371848.3 linkuse as main transcript	c.1476C>T	p.Asn492=	synonymous_variant	10/18	1		ENSP00000360914
WDR44	ENST00000371822.9 linkuse as main transcript	c.1701C>T	p.Asn567=	synonymous_variant	12/18	2		ENSP00000360887		Q5JSH3-4

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

14601

AN:

111683

Hom.:

786

Cov.:

AF XY:

0.129

AC XY:

4370

AN XY:

33873

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.0796

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.160

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.141

GnomAD3 exomes

AF:

0.171

AC:

31281

AN:

183148

Hom.:

2495

AF XY:

0.160

AC XY:

10832

AN XY:

67650

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.382

Gnomad ASJ exome

AF:

0.126

Gnomad EAS exome

AF:

0.189

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.131

AC:

143640

AN:

1096874

Hom.:

7382

Cov.:

AF XY:

0.131

AC XY:

47622

AN XY:

362992

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.373

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.179

Gnomad4 SAS exome

AF:

0.166

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.118

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.131

AC:

14630

AN:

111736

Hom.:

796

Cov.:

AF XY:

0.129

AC XY:

4384

AN XY:

33936

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.132

Hom.:

4869

Bravo

AF:

0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

1.4

DANN

Benign

0.66

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over