10-120852958-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_018117.12(WDR11):c.198+323G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,186 control chromosomes in the GnomAD database, including 2,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (2145 hom., cov: 33)
• Consequence: WDR11 NM_018117.12 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.925

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 10-120852958-G-A is Benign according to our data. Variant chr10-120852958-G-A is described in ClinVar as [Benign]. Clinvar id is 1269938.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR11	NM_018117.12	c.198+323G>A		intron_variant		ENST00000263461.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR11	ENST00000263461.11	c.198+323G>A		intron_variant		1	NM_018117.12	P1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23232 AN: 152068 Hom.: 2140 Cov.: 33

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.178

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23239 AN: 152186 Hom.: 2145 Cov.: 33 AF XY: 0.151 AC XY: 11263 AN XY: 74402

Gnomad4 AFR AF: 0.0701

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.181

Alfa AF: 0.173 Hom.: 331

Bravo AF: 0.144

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 05, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	6.0
Dann	Benign	0.81

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

Other links and lift over

dbSNP: rs41287984; hg19: chr10-122612470;