rs112459242

Variant names:

• chr10-120851418-G-A
• rs112459242
• NM_018117.12:c.-3G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-120851418-G-A
• chr10-120851418-G-C
• chr10-120851418-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_018117.12(WDR11):​c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,609,232 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0067 (17 hom., cov: 33)
  • Exomes 𝑓: 0.00095 (13 hom.)
• Consequence: WDR11 NM_018117.12 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.54
• 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP6: Variant 10-120851418-G-A is Benign according to our data. Variant chr10-120851418-G-A is described in ClinVar as Benign. ClinVar VariationId is 1177878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0067 (1020/152348) while in subpopulation AFR AF = 0.0224 (933/41572). AF 95% confidence interval is 0.0212. There are 17 homozygotes in GnomAd4. There are 473 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 17 AR,AD gene

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.-3G>A		5_prime_UTR	Exon 1 of 29	NP_060587.8
	WDR11-DT	NR_033850.1		n.-239C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11	ENST00000263461.11	TSL:1 MANE Select	c.-3G>A		5_prime_UTR	Exon 1 of 29	ENSP00000263461.5	Q9BZH6
	WDR11	ENST00000605543.5	TSL:2	n.-3G>A		non_coding_transcript_exon	Exon 1 of 22	ENSP00000475076.1	S4R451
	WDR11	ENST00000605543.5	TSL:2	n.-3G>A		5_prime_UTR	Exon 1 of 22	ENSP00000475076.1	S4R451

Frequencies

GnomAD3 genomes AF: 0.00668 AC: 1017 AN: 152230 Hom.: 17 Cov.: 33

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00366

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000323

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00181 AC: 430 AN: 238084 AF XY: 0.00142

Gnomad AFR exome AF: 0.0232

Gnomad AMR exome AF: 0.00155

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000487

Gnomad NFE exome AF: 0.000337

Gnomad OTH exome AF: 0.000859

GnomAD4 exome AF: 0.000954 AC: 1390 AN: 1456884 Hom.: 13 Cov.: 31 AF XY: 0.000840 AC XY: 608 AN XY: 724218

African (AFR) AF: 0.0250 AC: 835 AN: 33430

American (AMR) AF: 0.00175 AC: 77 AN: 44118

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25948

East Asian (EAS) AF: 0.00 AC: 0 AN: 39558

South Asian (SAS) AF: 0.0000235 AC: 2 AN: 85094

European-Finnish (FIN) AF: 0.000115 AC: 6 AN: 52126

Middle Eastern (MID) AF: 0.00174 AC: 10 AN: 5748

European-Non Finnish (NFE) AF: 0.000310 AC: 344 AN: 1110630

Other (OTH) AF: 0.00193 AC: 116 AN: 60232

GnomAD4 genome AF: 0.00670 AC: 1020 AN: 152348 Hom.: 17 Cov.: 33 AF XY: 0.00635 AC XY: 473 AN XY: 74506

African (AFR) AF: 0.0224 AC: 933 AN: 41572

American (AMR) AF: 0.00366 AC: 56 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10628

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000323 AC: 22 AN: 68034

Other (OTH) AF: 0.00284 AC: 6 AN: 2116

Alfa AF: 0.00412 Hom.: 5

Bravo AF: 0.00740

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	15
DANN	Benign	0.90
PhyloP100		1.5
PromoterAI		-0.29	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=300/0	polymorphism

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: rs112459242; hg19: chr10-122610930;