rs6560711

chr10-1122623-G-Achr10-1122623-G-Cchr10-1122623-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

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]

ACMG classification

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
WDR37	NM_014023.4	c.1104-1595G>A		intron_variant		ENST00000263150.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR37	ENST00000263150.9	c.1104-1595G>A		intron_variant		1	NM_014023.4	P1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124933 AN: 152196 Hom.: 51309 Cov.: 35

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

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

Other links and lift over

dbSNP: rs6560711; hg19: chr10-1168563;