10-1110225-T-C

Position:

• chr10-1110225-T-C

Variant summary

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

The NM_014023.4(WDR37):​c.1103+4958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,238 control chromosomes in the GnomAD database, including 60,390 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 0.89 (60390 hom., cov: 32)
• Consequence: WDR37 NM_014023.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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]

WDR37 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR37	NM_014023.4	c.1103+4958T>C		intron_variant		ENST00000263150.9	NP_054742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000263150.9	c.1103+4958T>C		intron_variant		1	NM_014023.4	ENSP00000263150.4

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135219 AN: 152120 Hom.: 60356 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.889 AC: 135313 AN: 152238 Hom.: 60390 Cov.: 32 AF XY: 0.890 AC XY: 66280 AN XY: 74450

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.956

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.895

Alfa AF: 0.922 Hom.: 99009

Bravo AF: 0.880

Asia WGS AF: 0.928 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.34

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: rs10794720; hg19: chr10-1156165;