rs2066987

Variant names:

• chr5-77560792-T-A
• rs2066987
• ENST00000509971.5:c.42+59687A>T

Variant summary

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

The ENST00000509971.5(WDR41):​c.42+59687A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 152,254 control chromosomes in the GnomAD database, including 488 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 0.069 (488 hom., cov: 32)
• Consequence: WDR41 ENST00000509971.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509971.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR41	ENST00000509971.5	TSL:3	c.42+59687A>T		intron	N/A	ENSP00000422922.1
	WDR41	ENST00000509858.5	TSL:3	n.99-20256A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10455 AN: 152136 Hom.: 485 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0687 AC: 10467 AN: 152254 Hom.: 488 Cov.: 32 AF XY: 0.0700 AC XY: 5213 AN XY: 74426

African (AFR) AF: 0.0786 AC: 3265 AN: 41564

American (AMR) AF: 0.141 AC: 2150 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3466

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5192

South Asian (SAS) AF: 0.0498 AC: 240 AN: 4820

European-Finnish (FIN) AF: 0.0529 AC: 562 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0576 AC: 3917 AN: 67992

Other (OTH) AF: 0.0595 AC: 126 AN: 2116

Alfa AF: 0.0624 Hom.: 41

Bravo AF: 0.0748

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.5
DANN	Benign	0.68
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2066987; hg19: chr5-76856617;