5-77512310-T-C

Variant names:

• chr5-77512310-T-C
• rs10514104
• ENST00000509971.5:c.43-22738A>G

Variant summary

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

The ENST00000509971.5(WDR41):​c.43-22738A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 131,950 control chromosomes in the GnomAD database, including 1,285 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 0.13 (1285 hom., cov: 26)
• Consequence: WDR41 ENST00000509971.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 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.43-22738A>G		intron	N/A	ENSP00000422922.1
	WDR41	ENST00000509858.5	TSL:3	n.178-22753A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 17410 AN: 131842 Hom.: 1282 Cov.: 26

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0644

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0543

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.132 AC: 17419 AN: 131950 Hom.: 1285 Cov.: 26 AF XY: 0.132 AC XY: 8448 AN XY: 64092

African (AFR) AF: 0.0389 AC: 1265 AN: 32558

American (AMR) AF: 0.121 AC: 1511 AN: 12534

Ashkenazi Jewish (ASJ) AF: 0.0644 AC: 210 AN: 3260

East Asian (EAS) AF: 0.148 AC: 724 AN: 4908

South Asian (SAS) AF: 0.184 AC: 788 AN: 4292

European-Finnish (FIN) AF: 0.181 AC: 1604 AN: 8874

Middle Eastern (MID) AF: 0.0537 AC: 13 AN: 242

European-Non Finnish (NFE) AF: 0.175 AC: 10968 AN: 62610

Other (OTH) AF: 0.125 AC: 233 AN: 1862

Alfa AF: 0.144 Hom.: 4637

Bravo AF: 0.105

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.51
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: rs10514104; hg19: chr5-76808135;