5-77432260-C-T

Variant names:

• chr5-77432260-C-T
• rs335632
• ENST00000502528.5:n.3252G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502528.5(WDR41):​n.3252G>A variant causes a non coding transcript exon 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 ENST00000502528.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
WDR41	NM_018268.4	c.*875G>A		3_prime_UTR_variant	Exon 13 of 13	ENST00000296679.9	NP_060738.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR41	ENST00000296679.9	c.*875G>A		3_prime_UTR_variant	Exon 13 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.971 AC: 40375 AN: 41574

American (AMR) AF: 0.895 AC: 13677 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3090 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5152 AN: 5188

South Asian (SAS) AF: 0.963 AC: 4649 AN: 4826

European-Finnish (FIN) AF: 0.864 AC: 9149 AN: 10590

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56432 AN: 68024

Other (OTH) AF: 0.887 AC: 1874 AN: 2112

Alfa AF: 0.854 Hom.: 80263

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
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs335632; hg19: chr5-76728085;