5-77449241-GAGGA-G

Variant names:

• chr5-77449241-GAGGA-G
• rs1610937
• NM_018268.4:c.697+515_697+518delTCCT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_018268.4(WDR41):​c.697+515_697+518delTCCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (28240 hom., cov: 0)
• Consequence: WDR41 NM_018268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 7 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018268.4. 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
	WDR41	NM_018268.4	MANE Select	c.697+515_697+518delTCCT		intron	N/A	NP_060738.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR41	ENST00000296679.9	TSL:1 MANE Select	c.697+515_697+518delTCCT		intron	N/A	ENSP00000296679.4	Q9HAD4-1
	WDR41	ENST00000502528.5	TSL:1	n.1694+515_1694+518delTCCT		intron	N/A
	WDR41	ENST00000862580.1		c.712+515_712+518delTCCT		intron	N/A	ENSP00000532639.1

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89435 AN: 151488 Hom.: 28193 Cov.: 0

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.591 AC: 89538 AN: 151604 Hom.: 28240 Cov.: 0 AF XY: 0.592 AC XY: 43829 AN XY: 74086

African (AFR) AF: 0.811 AC: 33510 AN: 41302

American (AMR) AF: 0.651 AC: 9916 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2374 AN: 3464

East Asian (EAS) AF: 0.588 AC: 3016 AN: 5126

South Asian (SAS) AF: 0.632 AC: 3040 AN: 4812

European-Finnish (FIN) AF: 0.446 AC: 4674 AN: 10490

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31095 AN: 67860

Other (OTH) AF: 0.598 AC: 1260 AN: 2108

Alfa AF: 0.527 Hom.: 2807

Bravo AF: 0.622

Asia WGS AF: 0.611 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1610937; hg19: chr5-76745066;