GeneBe

rs1610937

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018268.4(WDR41):​c.697+515_697+518del 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WDR41NM_018268.4 linkuse as main transcriptc.697+515_697+518del intron_variant ENST00000296679.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDR41ENST00000296679.9 linkuse as main transcriptc.697+515_697+518del intron_variant 1 NM_018268.4 P1Q9HAD4-1

Frequencies

GnomAD3 genomes
AF:
0.590
AC:
89435
AN:
151488
Hom.:
28193
Cov.:
0
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.811
Gnomad4 AMR
AF:
0.651
Gnomad4 ASJ
AF:
0.685
Gnomad4 EAS
AF:
0.588
Gnomad4 SAS
AF:
0.632
Gnomad4 FIN
AF:
0.446
Gnomad4 NFE
AF:
0.458
Gnomad4 OTH
AF:
0.598
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 v4.3

Name
Calibrated prediction
Score
Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1610937; hg19: chr5-76745066; API