Variant chr10-120852260-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018117.12(WDR11):c.87-264A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 423,394 control chromosomes in the GnomAD database, including 13,923 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6230 hom., cov: 32)

Exomes 𝑓: 0.23 ( 7693 hom. )

Consequence

WDR11
NM_018117.12 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.71

Variant links:

Genes affected

WDR11 (HGNC:13831): (WD repeat domain 11) 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. This gene is located in the chromosome 10q25-26 region, which is frequently deleted in gliomas and tumors of other tissues, and is disrupted by the t(10;19) translocation rearrangement in glioblastoma cells. The gene location suggests that it is a candidate gene for the tumor suppressor locus. [provided by RefSeq, Jul 2008]

WDR11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 10-120852260-A-T is Benign according to our data. Variant chr10-120852260-A-T is described in ClinVar as [Benign]. Clinvar id is 1287118.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11	NM_018117.12 linkuse as main transcript	c.87-264A>T		intron_variant		ENST00000263461.11	NP_060587.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11	ENST00000263461.11 linkuse as main transcript	c.87-264A>T		intron_variant		1	NM_018117.12	ENSP00000263461	P1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41030

AN:

151956

Hom.:

6214

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.314

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.0992

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.269

GnomAD4 exome

AF:

0.228

AC:

61938

AN:

271320

Hom.:

7693

Cov.:

AF XY:

0.229

AC XY:

33573

AN XY:

146288

show subpopulations

Gnomad4 AFR exome

AF:

0.406

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.266

Gnomad4 EAS exome

AF:

0.105

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.222

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.234

GnomAD4 genome

AF:

0.270

AC:

41083

AN:

152074

Hom.:

6230

Cov.:

AF XY:

0.263

AC XY:

19579

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.193

Gnomad4 ASJ

AF:

0.282

Gnomad4 EAS

AF:

0.0994

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.254

Hom.:

654

Bravo

AF:

0.275

Asia WGS

AF:

0.167

AC:

583

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.78

DANN

Benign

0.43

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over