rs1610937

chr5-77449241-GAGGA-Gchr5-77449241-GAGGA-GAGGAAGGA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018268.4(WDR41):c.697+515_697+518del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,604 control chromosomes in the GnomAD database, including 28,240 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (28240 hom., cov: 0)
• Consequence: WDR41 NM_018268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

WDR41 (HGNC:25601): (WD repeat domain 41) Contributes to guanyl-nucleotide exchange factor activity. Involved in regulation of autophagy. Located in cytoplasm. Part of guanyl-nucleotide exchange factor complex. Colocalizes with Atg1/ULK1 kinase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR41	NM_018268.4	c.697+515_697+518del		intron_variant		ENST00000296679.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR41	ENST00000296679.9	c.697+515_697+518del		intron_variant		1	NM_018268.4	P1

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89435 AN: 151488 Hom.: 28193 Cov.: 0

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.597

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.591 AC: 89538 AN: 151604 Hom.: 28240 Cov.: 0 AF XY: 0.592 AC XY: 43829 AN XY: 74086

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.598

Alfa AF: 0.527 Hom.: 2807

Bravo AF: 0.622

Asia WGS AF: 0.611 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

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: rs1610937; hg19: chr5-76745066;