chr10-120851281-C-T

Position:

• chr10-120851281-C-T

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.177G>A 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 0.0183 in 774,650 control chromosomes in the GnomAD database, including 1,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.062 (959 hom., cov: 33)
  • Exomes 𝑓: 0.0077 (402 hom.)
• Consequence: WDR11-DT ENST00000630905.5 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.224

Genes affected

WDR11-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 10-120851281-C-T is Benign according to our data. Variant chr10-120851281-C-T is described in ClinVar as [Benign]. Clinvar id is 1259101.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.120851281C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000630905.5	n.177G>A		non_coding_transcript_exon_variant	1/3	2
WDR11	ENST00000605202.5	n.-24C>T		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.0617 AC: 9394 AN: 152204 Hom.: 958 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0249

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00103

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.000867

Gnomad OTH AF: 0.0497

GnomAD4 exome AF: 0.00770 AC: 4792 AN: 622328 Hom.: 402 Cov.: 8 AF XY: 0.00631 AC XY: 2081 AN XY: 329948

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.0150

Gnomad4 ASJ exome AF: 0.00262

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000466

Gnomad4 FIN exome AF: 0.0000830

Gnomad4 NFE exome AF: 0.000663

Gnomad4 OTH exome AF: 0.0159

GnomAD4 genome AF: 0.0618 AC: 9417 AN: 152322 Hom.: 959 Cov.: 33 AF XY: 0.0601 AC XY: 4475 AN XY: 74490

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0249

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000867

Gnomad4 OTH AF: 0.0491

Alfa AF: 0.0296 Hom.: 62

Bravo AF: 0.0700

Asia WGS AF: 0.00895 AC: 31 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	clinical testing	GeneDx	Nov 15, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.7
DANN	Benign	0.83

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: rs17100983; hg19: chr10-122610793;