rs10886800

Positions:

• chr10-120908900-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_018117.12(WDR11):​c.*187G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 645,812 control chromosomes in the GnomAD database, including 12,502 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (2435 hom., cov: 33)
  • Exomes 𝑓: 0.19 (10067 hom.)
• Consequence: WDR11 NM_018117.12 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.353

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]

LOC105378519 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 10-120908900-G-A is Benign according to our data. Variant chr10-120908900-G-A is described in ClinVar as [Benign]. Clinvar id is 1283844.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11	NM_018117.12	c.*187G>A		3_prime_UTR_variant	29/29	ENST00000263461.11	NP_060587.8
LOC105378519	XR_001747609.2	n.541-6558C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11	ENST00000263461.11	c.*187G>A		3_prime_UTR_variant	29/29	1	NM_018117.12	ENSP00000263461	P1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23871 AN: 152068 Hom.: 2435 Cov.: 33

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.190 AC: 93840 AN: 493626 Hom.: 10067 Cov.: 6 AF XY: 0.188 AC XY: 49327 AN XY: 262582

Gnomad4 AFR exome AF: 0.0542

Gnomad4 AMR exome AF: 0.352

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.157 AC: 23865 AN: 152186 Hom.: 2435 Cov.: 33 AF XY: 0.157 AC XY: 11683 AN XY: 74394

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.152

Alfa AF: 0.194 Hom.: 1490

Bravo AF: 0.167

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.59
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10886800; hg19: chr10-122668412;