rs251470

Variant names:

• chr5-77482660-C-A
• rs251470
• NM_018268.4:c.167+6797G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_018268.4(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 NM_018268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 5 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]

LOC124901009 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
WDR41	NM_018268.4	c.167+6797G>T		intron_variant	Intron 2 of 12	ENST00000296679.9	NP_060738.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR41	ENST00000296679.9	c.167+6797G>T		intron_variant	Intron 2 of 12	1	NM_018268.4	ENSP00000296679.4

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

African (AFR) AF: 0.797 AC: 33055 AN: 41452

American (AMR) AF: 0.630 AC: 9611 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2305 AN: 3466

East Asian (EAS) AF: 0.591 AC: 3052 AN: 5162

South Asian (SAS) AF: 0.604 AC: 2903 AN: 4808

European-Finnish (FIN) AF: 0.439 AC: 4622 AN: 10518

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29406 AN: 67920

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.454 Hom.: 7866

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
PhyloP100		0.33
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: rs251470; hg19: chr5-76778485;