Variant 10-120858636-G-C 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.199-7G>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,613,528 control chromosomes in the GnomAD database, including 31,384 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2432 hom., cov: 33)

Exomes 𝑓: 0.19 ( 28952 hom. )

Consequence

WDR11
NM_018117.12 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0003091

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.755

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 10-120858636-G-C is Benign according to our data. Variant chr10-120858636-G-C is described in ClinVar as [Benign]. Clinvar id is 1261179.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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.199-7G>C		splice_region_variant, splice_polypyrimidine_tract_variant, 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.199-7G>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_018117.12	ENSP00000263461	P1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23867

AN:

152092

Hom.:

2432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.154

GnomAD3 exomes

AF:

0.209

AC:

52407

AN:

251202

Hom.:

6764

AF XY:

0.200

AC XY:

27188

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.0511

Gnomad AMR exome

AF:

0.393

Gnomad ASJ exome

AF:

0.250

Gnomad EAS exome

AF:

0.342

Gnomad SAS exome

AF:

0.164

Gnomad FIN exome

AF:

0.117

Gnomad NFE exome

AF:

0.180

Gnomad OTH exome

AF:

0.189

GnomAD4 exome

AF:

0.191

AC:

278442

AN:

1461318

Hom.:

28952

Cov.:

AF XY:

0.189

AC XY:

137048

AN XY:

726964

show subpopulations

Gnomad4 AFR exome

AF:

0.0473

Gnomad4 AMR exome

AF:

0.382

Gnomad4 ASJ exome

AF:

0.252

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.164

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.187

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.157

AC:

23860

AN:

152210

Hom.:

2432

Cov.:

AF XY:

0.157

AC XY:

11685

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0547

Gnomad4 AMR

AF:

0.276

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.338

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.180

Hom.:

899

Bravo

AF:

0.167

Asia WGS

AF:

0.245

AC:

854

AN:

3478

EpiCase

AF:

0.169

EpiControl

AF:

0.171

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	- -

Hypogonadotropic hypogonadism 14 with or without anosmia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.5

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00031

dbscSNV1_RF

Benign

0.064

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