10-120851275-T-A

Position:

• chr10-120851275-T-A

Variant summary

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

The ENST00000630905.5(WDR11-DT):​n.183A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 729,742 control chromosomes in the GnomAD database, including 22,820 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.28 (6641 hom., cov: 33)
  • Exomes 𝑓: 0.23 (16179 hom.)
• Consequence: WDR11-DT ENST00000630905.5 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.679

Genes affected

WDR11-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 10-120851275-T-A is Benign according to our data. Variant chr10-120851275-T-A is described in ClinVar as [Benign]. Clinvar id is 1183546.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.120851275T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000630905.5	n.183A>T		non_coding_transcript_exon_variant	1/3	2
WDR11	ENST00000605202.5	n.-30T>A		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42192 AN: 152044 Hom.: 6625 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.228 AC: 131838 AN: 577580 Hom.: 16179 Cov.: 7 AF XY: 0.229 AC XY: 70278 AN XY: 306760

Gnomad4 AFR exome AF: 0.432

Gnomad4 AMR exome AF: 0.137

Gnomad4 ASJ exome AF: 0.257

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.232

Gnomad4 FIN exome AF: 0.222

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.237

GnomAD4 genome AF: 0.278 AC: 42246 AN: 152162 Hom.: 6641 Cov.: 33 AF XY: 0.271 AC XY: 20153 AN XY: 74396

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.277

Alfa AF: 0.260 Hom.: 700

Bravo AF: 0.283

Asia WGS AF: 0.170 AC: 593 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 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.3
DANN	Benign	0.75

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: rs12267610; hg19: chr10-122610787;