Genetic Variant WDR37:c.-153C>G (chr10-1056856-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.790

Publications

6 publications found

Variant links:

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 links:

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]

IDI1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	c.-153C>G		5_prime_UTR_variant	Exon 1 of 14	ENST00000263150.9	NP_054742.2	Q9Y2I8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR37	ENST00000263150.9 link	c.-153C>G		5_prime_UTR_variant	Exon 1 of 14	1	NM_014023.4	ENSP00000263150.4		Q9Y2I8-1

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80187

AN:

151736

Hom.:

21599

Cov.:

show subpopulations

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:

AN:

152

Hom.:

Cov.:

AF XY:

0.533

AC XY:

AN XY:

120

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.667

AC:

AN:

South Asian (SAS)

AF:

0.563

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.549

AC:

AN:

122

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.528

AC:

80254

AN:

151854

Hom.:

21627

Cov.:

AF XY:

0.532

AC XY:

39453

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.637

AC:

26377

AN:

41410

American (AMR)

AF:

0.489

AC:

7482

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.443

AC:

1538

AN:

3468

East Asian (EAS)

AF:

0.581

AC:

2961

AN:

5096

South Asian (SAS)

AF:

0.592

AC:

2853

AN:

4820

European-Finnish (FIN)

AF:

0.529

AC:

5587

AN:

10558

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.470

AC:

31928

AN:

67898

Other (OTH)

AF:

0.504

AC:

1064

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1917

3834

5752

7669

9586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

694

1388

2082

2776

3470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.52

PhyloP100

-0.79

PromoterAI

0.079

Neutral

(source)

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over