rs10903366

Positions:

• chr10-1093885-A-G
• chr10-1093885-A-T

Variant summary

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

The NM_014023.4(WDR37):​c.649+389A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,148 control chromosomes in the GnomAD database, including 12,130 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 0.39 (12130 hom., cov: 33)
• Consequence: WDR37 NM_014023.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR37	NM_014023.4	c.649+389A>G		intron_variant		ENST00000263150.9	NP_054742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000263150.9	c.649+389A>G		intron_variant		1	NM_014023.4	ENSP00000263150	P1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59765 AN: 152030 Hom.: 12106 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.393 AC: 59838 AN: 152148 Hom.: 12130 Cov.: 33 AF XY: 0.393 AC XY: 29260 AN XY: 74374

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.406

Alfa AF: 0.368 Hom.: 1340

Bravo AF: 0.409

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.60

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: rs10903366; hg19: chr10-1139825;