rs251470

Positions:

• chr5-77482660-C-A
• chr5-77482660-C-G
• chr5-77482660-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000296679.9(WDR41):​c.167+6797G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,900 control chromosomes in the GnomAD database, including 26,698 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (26698 hom., cov: 30)
• Consequence: WDR41 ENST00000296679.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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]

LOC124901009 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR41	NM_018268.4	c.167+6797G>T		intron_variant		ENST00000296679.9	NP_060738.2
LOC124901009	XR_007058828.1	n.326G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR41	ENST00000296679.9	c.167+6797G>T		intron_variant		1	NM_018268.4	ENSP00000296679	P1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86648 AN: 151780 Hom.: 26653 Cov.: 30

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.571 AC: 86750 AN: 151900 Hom.: 26698 Cov.: 30 AF XY: 0.573 AC XY: 42489 AN XY: 74214

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.574

Alfa AF: 0.447 Hom.: 6715

Bravo AF: 0.600

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.75

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: rs251470; hg19: chr5-76778485;