10-120852260-A-T

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.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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.71

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=-0.84).
• 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_single_submitter, 1 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	UniProt
WDR11	NM_018117.12	c.87-264A>T		intron_variant		ENST00000263461.11

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41030 AN: 151956 Hom.: 6214 Cov.: 32

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.: 2 AF XY: 0.229 AC XY: 33573 AN XY: 146288

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.: 32 AF XY: 0.263 AC XY: 19579 AN XY: 74342

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2018

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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

Other links and lift over

dbSNP: rs7917351; hg19: chr10-122611772;