chr10-1110225-T-C

Variant names:

• chr10-1110225-T-C
• rs10794720
• NM_014023.4:c.1103+4958T>C

Variant summary

Our verdict is Benign. The variant received -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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
WDR37	NM_014023.4	c.1103+4958T>C		intron_variant	Intron 11 of 13	ENST00000263150.9	NP_054742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000263150.9	c.1103+4958T>C		intron_variant	Intron 11 of 13	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

African (AFR) AF: 0.796 AC: 33035 AN: 41502

American (AMR) AF: 0.896 AC: 13714 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3309 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4652 AN: 5176

South Asian (SAS) AF: 0.956 AC: 4617 AN: 4828

European-Finnish (FIN) AF: 0.933 AC: 9901 AN: 10614

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63145 AN: 68028

Other (OTH) AF: 0.895 AC: 1893 AN: 2114

Alfa AF: 0.913 Hom.: 148559

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
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs10794720; hg19: chr10-1156165;