Variant rs3745032 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_015285.3(WDR7):c.*112C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 1,336,130 control chromosomes in the GnomAD database, including 501 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 0.021 ( 37 hom., cov: 32)

Exomes 𝑓: 0.025 ( 464 hom. )

Consequence

WDR7
NM_015285.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.62

Variant links:

Genes affected

WDR7 (HGNC:13490): (WD repeat domain 7) 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) that 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. The encoded protein forms the beta subunit of rabconnectin-3 and binds directly with Rab3A GDP/GTP exchange protein and indirectly with Rab3A GDP/GTP activating protein; these proteins are regulators of Rab3 small G protein family members involved in control of the calcium-dependant exocytosis of neurotransmitters. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

WDR7 links:

WDR7 (HGNC:):

WDR7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0208 (3039/145962) while in subpopulation EAS AF= 0.0506 (260/5140). AF 95% confidence interval is 0.0455. There are 37 homozygotes in gnomad4. There are 1427 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3039 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR7	NM_015285.3 linkuse as main transcript	c.*112C>T		3_prime_UTR_variant	28/28	ENST00000254442.8	NP_056100.2	Q9Y4E6-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
WDR7	ENST00000254442.8 linkuse as main transcript	c.*112C>T	3_prime_UTR_variant	28/28	1	NM_015285.3	ENSP00000254442.3	Q9Y4E6-1
WDR7	ENST00000357574.7 linkuse as main transcript	c.*112C>T	3_prime_UTR_variant	27/27	5		ENSP00000350187.2	Q9Y4E6-2
WDR7	ENST00000589935.1 linkuse as main transcript	c.*112C>T	downstream_gene_variant		4		ENSP00000467485.1	K7EPQ4

Frequencies

GnomAD3 genomes

AF:

0.0208

AC:

3037

AN:

145852

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00656

Gnomad AMI

AF:

0.0314

Gnomad AMR

AF:

0.0265

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.0503

Gnomad SAS

AF:

0.00700

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.00333

Gnomad NFE

AF:

0.0290

Gnomad OTH

AF:

0.0150

GnomAD4 exome

AF:

0.0254

AC:

30193

AN:

1190168

Hom.:

464

Cov.:

AF XY:

0.0246

AC XY:

14440

AN XY:

585964

show subpopulations

Gnomad4 AFR exome

AF:

0.00395

Gnomad4 AMR exome

AF:

0.0304

Gnomad4 ASJ exome

AF:

0.0138

Gnomad4 EAS exome

AF:

0.0504

Gnomad4 SAS exome

AF:

0.00571

Gnomad4 FIN exome

AF:

0.0125

Gnomad4 NFE exome

AF:

0.0275

Gnomad4 OTH exome

AF:

0.0194

GnomAD4 genome

AF:

0.0208

AC:

3039

AN:

145962

Hom.:

Cov.:

AF XY:

0.0200

AC XY:

1427

AN XY:

71474

show subpopulations

Gnomad4 AFR

AF:

0.00654

Gnomad4 AMR

AF:

0.0266

Gnomad4 ASJ

AF:

0.0170

Gnomad4 EAS

AF:

0.0506

Gnomad4 SAS

AF:

0.00701

Gnomad4 FIN

AF:

0.0104

Gnomad4 NFE

AF:

0.0290

Gnomad4 OTH

AF:

0.0149

Alfa

AF:

0.0209

Hom.:

Bravo

AF:

0.0200

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over