chr10-1132954-C-T

Position:

• chr10-1132954-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000704674.1	c.162+7930C>T		intron_variant				ENSP00000515987
WDR37	ENST00000704739.1	c.*374+7930C>T		intron_variant, NMD_transcript_variant				ENSP00000516016
WDR37	ENST00000704675.1	n.762+7930C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.413

Alfa AF: 0.425 Hom.: 2010

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4256905; hg19: chr10-1178894;