rs35692153

Variant names:

• chr10-120851471-G-T
• rs35692153
• NM_018117.12:c.51G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-120851471-G-T
• chr10-120851471-G-A

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_018117.12(WDR11):​c.51G>T​(p.Gly17Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,612,208 control chromosomes in the GnomAD database, including 1,467 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.055 (772 hom., cov: 33)
  • Exomes 𝑓: 0.0059 (695 hom.)
• Consequence: WDR11 NM_018117.12 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.285
• Publications: 0 publications found

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-DT (HGNC:27437): (WDR11 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 10-120851471-G-T is Benign according to our data. Variant chr10-120851471-G-T is described in ClinVar as Benign. ClinVar VariationId is 1279300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.285 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018117.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11	NM_018117.12	MANE Select	c.51G>T	p.Gly17Gly	synonymous	Exon 1 of 29	NP_060587.8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11	ENST00000263461.11	TSL:1 MANE Select	c.51G>T	p.Gly17Gly	synonymous	Exon 1 of 29	ENSP00000263461.5	Q9BZH6
	WDR11	ENST00000605543.5	TSL:2	n.51G>T		non_coding_transcript_exon	Exon 1 of 22	ENSP00000475076.1	S4R451
	WDR11	ENST00000605069.5	TSL:4	n.80G>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8352 AN: 152176 Hom.: 772 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.000794

Gnomad OTH AF: 0.0459

GnomAD2 exomes AF: 0.0127 AC: 3077 AN: 241618 AF XY: 0.00958

Gnomad AFR exome AF: 0.173

Gnomad AMR exome AF: 0.0110

Gnomad ASJ exome AF: 0.00315

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000741

Gnomad OTH exome AF: 0.00727

GnomAD4 exome AF: 0.00586 AC: 8553 AN: 1459916 Hom.: 695 Cov.: 31 AF XY: 0.00500 AC XY: 3633 AN XY: 726164

African (AFR) AF: 0.195 AC: 6512 AN: 33420

American (AMR) AF: 0.0123 AC: 547 AN: 44604

Ashkenazi Jewish (ASJ) AF: 0.00257 AC: 67 AN: 26064

East Asian (EAS) AF: 0.00 AC: 0 AN: 39654

South Asian (SAS) AF: 0.000315 AC: 27 AN: 85806

European-Finnish (FIN) AF: 0.0000571 AC: 3 AN: 52508

Middle Eastern (MID) AF: 0.0106 AC: 61 AN: 5760

European-Non Finnish (NFE) AF: 0.000534 AC: 594 AN: 1111772

Other (OTH) AF: 0.0123 AC: 742 AN: 60328

GnomAD4 genome AF: 0.0549 AC: 8364 AN: 152292 Hom.: 772 Cov.: 33 AF XY: 0.0532 AC XY: 3961 AN XY: 74472

African (AFR) AF: 0.189 AC: 7851 AN: 41536

American (AMR) AF: 0.0225 AC: 345 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.000794 AC: 54 AN: 68028

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0266 Hom.: 108

Bravo AF: 0.0626

Asia WGS AF: 0.00693 AC: 24 AN: 3478

EpiCase AF: 0.000763

EpiControl AF: 0.000774

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not provided (3)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.28
PromoterAI		-0.16	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs35692153; hg19: chr10-122610983;