rs6560711

Variant summary

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

The NM_014023.4(WDR37):​c.1104-1595G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,314 control chromosomes in the GnomAD database, including 51,350 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 0.82 ( 51350 hom., cov: 35)

Consequence

WDR37
NM_014023.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.932
Variant links:
Genes affected
WDR37 (HGNC:31406): (WD repeat domain 37) 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. [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=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WDR37NM_014023.4 linkuse as main transcriptc.1104-1595G>A intron_variant ENST00000263150.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDR37ENST00000263150.9 linkuse as main transcriptc.1104-1595G>A intron_variant 1 NM_014023.4 P1Q9Y2I8-1

Frequencies

GnomAD3 genomes
AF:
0.821
AC:
124933
AN:
152196
Hom.:
51309
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.804
Gnomad AMI
AF:
0.654
Gnomad AMR
AF:
0.802
Gnomad ASJ
AF:
0.824
Gnomad EAS
AF:
0.803
Gnomad SAS
AF:
0.813
Gnomad FIN
AF:
0.816
Gnomad MID
AF:
0.810
Gnomad NFE
AF:
0.840
Gnomad OTH
AF:
0.815
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.821
AC:
125035
AN:
152314
Hom.:
51350
Cov.:
35
AF XY:
0.820
AC XY:
61079
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.804
Gnomad4 AMR
AF:
0.803
Gnomad4 ASJ
AF:
0.824
Gnomad4 EAS
AF:
0.803
Gnomad4 SAS
AF:
0.813
Gnomad4 FIN
AF:
0.816
Gnomad4 NFE
AF:
0.840
Gnomad4 OTH
AF:
0.817
Alfa
AF:
0.804
Hom.:
5294
Bravo
AF:
0.815
Asia WGS
AF:
0.825
AC:
2869
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.30
DANN
Benign
0.54

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: rs6560711; hg19: chr10-1168563; API