rs1009829

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_024452048.2(WDR4):​c.-350+4618C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,240 control chromosomes in the GnomAD database, including 33,205 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 0.64 ( 33204 hom., cov: 34)
Exomes 𝑓: 0.75 ( 1 hom. )

Consequence

WDR4
XM_024452048.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.882
Variant links:
Genes affected
WDR4 (HGNC:12756): (WD repeat domain 4) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This gene is excluded as a candidate for a form of nonsyndromic deafness (DFNB10), but is still a candidate for other disorders mapped to 21q22.3 as well as for the development of Down syndrome phenotypes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012]
NDUFV3 (HGNC:7719): (NADH:ubiquinone oxidoreductase subunit V3) The protein encoded by this gene is one of at least forty-one subunits that make up the NADH-ubiquinone oxidoreductase complex. This complex is part of the mitochondrial respiratory chain and serves to catalyze the rotenone-sensitive oxidation of NADH and the reduction of ubiquinone. The encoded protein is one of three proteins found in the flavoprotein fraction of the complex. The specific function of the encoded protein is unknown. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDR4XM_024452048.2 linkc.-350+4618C>T intron_variant Intron 2 of 11 XP_024307816.1
LOC105372817XR_937765.3 linkn.235-26G>A intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NDUFV3ENST00000460259.1 linkn.413-26G>A intron_variant Intron 2 of 5 2

Frequencies

GnomAD3 genomes
AF:
0.643
AC:
97779
AN:
152118
Hom.:
33151
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.857
Gnomad AMI
AF:
0.603
Gnomad AMR
AF:
0.443
Gnomad ASJ
AF:
0.567
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.558
Gnomad FIN
AF:
0.626
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.595
Gnomad OTH
AF:
0.582
GnomAD4 exome
AF:
0.750
AC:
3
AN:
4
Hom.:
1
Cov.:
0
AF XY:
0.750
AC XY:
3
AN XY:
4
show subpopulations
Gnomad4 NFE exome
AF:
0.750
GnomAD4 genome
AF:
0.643
AC:
97883
AN:
152236
Hom.:
33204
Cov.:
34
AF XY:
0.639
AC XY:
47530
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.857
Gnomad4 AMR
AF:
0.443
Gnomad4 ASJ
AF:
0.567
Gnomad4 EAS
AF:
0.339
Gnomad4 SAS
AF:
0.558
Gnomad4 FIN
AF:
0.626
Gnomad4 NFE
AF:
0.595
Gnomad4 OTH
AF:
0.585
Alfa
AF:
0.633
Hom.:
4160
Bravo
AF:
0.634
Asia WGS
AF:
0.462
AC:
1613
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.51
DANN
Benign
0.44

Splicing

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: rs1009829; hg19: chr21-44306885; API