chrX-118396949-GT-G

Position:

• chrX-118396949-GT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_019045.5(WDR44):​c.1054-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 592,229 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00087 (0 hom., 1 hem., cov: 21)
  • Exomes 𝑓: 0.11 (0 hom. 3 hem.)
• Consequence: WDR44 NM_019045.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.384

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-118396949-GT-G is Benign according to our data. Variant chrX-118396949-GT-G is described in ClinVar as [Benign]. Clinvar id is 1301422.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR44	NM_019045.5	c.1054-9delT		intron_variant		ENST00000254029.8	NP_061918.3
WDR44	NM_001184965.2	c.1054-9delT		intron_variant			NP_001171894.1
WDR44	NM_001184966.1	c.979-9delT		intron_variant			NP_001171895.1
WDR44	XM_011531353.4	c.979-9delT		intron_variant			XP_011529655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR44	ENST00000254029.8	c.1054-9delT		intron_variant		1	NM_019045.5	ENSP00000254029.3
WDR44	ENST00000371825.7	c.1054-9delT		intron_variant		1		ENSP00000360890.3
WDR44	ENST00000371848.3	c.751-9delT		intron_variant		1		ENSP00000360914.3
WDR44	ENST00000371822.9	c.979-9delT		intron_variant		2		ENSP00000360887.5

Frequencies

GnomAD3 genomes AF: 0.000869 AC: 88 AN: 101282 Hom.: 0 Cov.: 21 AF XY: 0.0000360 AC XY: 1 AN XY: 27776

Gnomad AFR AF: 0.000283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000854

Gnomad ASJ AF: 0.000404

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00994

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000610

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.247 AC: 9167 AN: 37178 Hom.: 0 AF XY: 0.000271 AC XY: 1 AN XY: 3686

Gnomad AFR exome AF: 0.227

Gnomad AMR exome AF: 0.290

Gnomad ASJ exome AF: 0.325

Gnomad EAS exome AF: 0.257

Gnomad SAS exome AF: 0.297

Gnomad FIN exome AF: 0.177

Gnomad NFE exome AF: 0.236

Gnomad OTH exome AF: 0.257

GnomAD4 exome AF: 0.106 AC: 52119 AN: 490958 Hom.: 0 Cov.: 0 AF XY: 0.0000208 AC XY: 3 AN XY: 144400

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.171

Gnomad4 ASJ exome AF: 0.153

Gnomad4 EAS exome AF: 0.155

Gnomad4 SAS exome AF: 0.0932

Gnomad4 FIN exome AF: 0.148

Gnomad4 NFE exome AF: 0.0990

Gnomad4 OTH exome AF: 0.126

GnomAD4 genome AF: 0.000869 AC: 88 AN: 101271 Hom.: 0 Cov.: 21 AF XY: 0.0000360 AC XY: 1 AN XY: 27785

Gnomad4 AFR AF: 0.000283

Gnomad4 AMR AF: 0.000853

Gnomad4 ASJ AF: 0.000404

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00994

Gnomad4 NFE AF: 0.000610

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs762713572; hg19: chrX-117530912;