chr10-120909092-G-A

Position:

• chr10-120909092-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018117.12(WDR11):​c.*379G>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 0.319 in 264,386 control chromosomes in the GnomAD database, including 14,074 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (7645 hom., cov: 33)
  • Exomes 𝑓: 0.33 (6429 hom.)
• Consequence: WDR11 NM_018117.12 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11	NM_018117.12	c.*379G>A		3_prime_UTR_variant	29/29	ENST00000263461.11	NP_060587.8
LOC105378519	XR_001747609.2	n.541-6750C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11	ENST00000263461.11	c.*379G>A		3_prime_UTR_variant	29/29	1	NM_018117.12	ENSP00000263461	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47256 AN: 151974 Hom.: 7639 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.329 AC: 36948 AN: 112294 Hom.: 6429 Cov.: 0 AF XY: 0.329 AC XY: 19470 AN XY: 59182

Gnomad4 AFR exome AF: 0.196

Gnomad4 AMR exome AF: 0.468

Gnomad4 ASJ exome AF: 0.401

Gnomad4 EAS exome AF: 0.404

Gnomad4 SAS exome AF: 0.313

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.324

Gnomad4 OTH exome AF: 0.329

GnomAD4 genome AF: 0.311 AC: 47284 AN: 152092 Hom.: 7645 Cov.: 33 AF XY: 0.310 AC XY: 23054 AN XY: 74334

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.317

Alfa AF: 0.336 Hom.: 8835

Bravo AF: 0.318

Asia WGS AF: 0.375 AC: 1305 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.8
DANN	Benign	0.61

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: rs1045154; hg19: chr10-122668604;