10-120909270-G-T

Position:

• chr10-120909270-G-T

Variant summary

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

The NM_018117.12(WDR11):​c.*557G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 154,886 control chromosomes in the GnomAD database, including 7,777 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 (7629 hom., cov: 33)
  • Exomes 𝑓: 0.30 (148 hom.)
• Consequence: WDR11 NM_018117.12 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.861

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• 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.*557G>T		3_prime_UTR_variant	29/29	ENST00000263461.11	NP_060587.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11	ENST00000263461.11	c.*557G>T		3_prime_UTR_variant	29/29	1	NM_018117.12	ENSP00000263461.5
WDR11	ENST00000497136.6	n.*3505G>T		non_coding_transcript_exon_variant	26/26	1		ENSP00000474595.1
WDR11	ENST00000497136.6	n.*3505G>T		3_prime_UTR_variant	26/26	1		ENSP00000474595.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47225 AN: 151654 Hom.: 7623 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.303 AC: 942 AN: 3114 Hom.: 148 Cov.: 0 AF XY: 0.295 AC XY: 490 AN XY: 1660

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.257

Gnomad4 FIN exome AF: 0.280

Gnomad4 NFE exome AF: 0.305

Gnomad4 OTH exome AF: 0.240

GnomAD4 genome AF: 0.311 AC: 47253 AN: 151772 Hom.: 7629 Cov.: 33 AF XY: 0.311 AC XY: 23039 AN XY: 74150

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.317

Alfa AF: 0.325 Hom.: 1774

Bravo AF: 0.318

Asia WGS AF: 0.376 AC: 1308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.7
DANN	Benign	0.65

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: rs1045170; hg19: chr10-122668782;