rs4256905

Variant names:

• chr10-1132954-C-T
• rs4256905
• ENST00000704674.1:c.162+7930C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000704674.1(WDR37):​c.162+7930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,190 control chromosomes in the GnomAD database, including 13,721 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 0.42 (13721 hom., cov: 34)
• Consequence: WDR37 ENST00000704674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• neurooculocardiogenitourinary syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000704674.1	c.162+7930C>T		intron_variant	Intron 12 of 12			ENSP00000515987.1
WDR37	ENST00000704675.1	n.762+7930C>T		intron_variant	Intron 5 of 5
WDR37	ENST00000704739.1	n.*374+7930C>T		intron_variant	Intron 11 of 11			ENSP00000516016.1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64170 AN: 152072 Hom.: 13714 Cov.: 34

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.422 AC: 64204 AN: 152190 Hom.: 13721 Cov.: 34 AF XY: 0.419 AC XY: 31145 AN XY: 74410

African (AFR) AF: 0.353 AC: 14647 AN: 41506

American (AMR) AF: 0.439 AC: 6720 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2244 AN: 5186

South Asian (SAS) AF: 0.302 AC: 1459 AN: 4826

European-Finnish (FIN) AF: 0.457 AC: 4833 AN: 10586

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31458 AN: 68006

Other (OTH) AF: 0.413 AC: 872 AN: 2110

Alfa AF: 0.423 Hom.: 2066

Bravo AF: 0.424

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.94
DANN	Benign	0.51
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4256905; hg19: chr10-1178894;