rs35656218

Variant names:

• chr10-1056856-C-G
• rs35656218
• NM_014023.4:c.-153C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-1056856-C-G
• chr10-1056856-C-T

Variant summary

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

The NM_014023.4(WDR37):​c.-153C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,006 control chromosomes in the GnomAD database, including 21,653 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 0.53 (21627 hom., cov: 31)
  • Exomes 𝑓: 0.56 (26 hom.)
• Consequence: WDR37 NM_014023.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

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]

IDI1 (HGNC:5387): (isopentenyl-diphosphate delta isomerase 1) IDI1 encodes a peroxisomally-localized enzyme that catalyzes the interconversion of isopentenyl diphosphate (IPP) to its highly electrophilic isomer, dimethylallyl diphosphate (DMAPP), which are the substrates for the successive reaction that results in the synthesis of farnesyl diphosphate and, ultimately, cholesterol. It has been shown in peroxisomal deficiency diseases such as Zellweger syndrome and neonatal adrenoleukodystrophy that there is reduction in IPP isomerase activity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR37	NM_014023.4	c.-153C>G		5_prime_UTR_variant	Exon 1 of 14	ENST00000263150.9	NP_054742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000263150	c.-153C>G		5_prime_UTR_variant	Exon 1 of 14	1	NM_014023.4	ENSP00000263150.4

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80187 AN: 151736 Hom.: 21599 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.499

GnomAD4 exome AF: 0.559 AC: 85 AN: 152 Hom.: 26 Cov.: 0 AF XY: 0.533 AC XY: 64 AN XY: 120

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.667

Gnomad4 SAS exome AF: 0.563

Gnomad4 NFE exome AF: 0.549

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.528 AC: 80254 AN: 151854 Hom.: 21627 Cov.: 31 AF XY: 0.532 AC XY: 39453 AN XY: 74200

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.504

Alfa AF: 0.511 Hom.: 2494

Bravo AF: 0.526

Asia WGS AF: 0.606 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.0
DANN	Benign	0.52
RBP_binding_hub_radar		0.67
RBP_regulation_power_radar		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs35656218; hg19: chr10-1102796;