5-77432260-C-T

Position:

• chr5-77432260-C-T

Variant summary

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

The NM_018268.4(WDR41):​c.*875G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,282 control chromosomes in the GnomAD database, including 60,633 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 0.89 (60632 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: WDR41 NM_018268.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

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]

WDR41 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR41	NM_018268.4	c.*875G>A		3_prime_UTR_variant	13/13	ENST00000296679.9	NP_060738.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR41	ENST00000296679	c.*875G>A		3_prime_UTR_variant	13/13	1	NM_018268.4	ENSP00000296679.4

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135350 AN: 152162 Hom.: 60565 Cov.: 33

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.886

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.890 AC: 135477 AN: 152280 Hom.: 60632 Cov.: 33 AF XY: 0.892 AC XY: 66377 AN XY: 74442

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.887

Alfa AF: 0.846 Hom.: 53777

Bravo AF: 0.897

Asia WGS AF: 0.969 AC: 3371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.35

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: rs335632; hg19: chr5-76728085;