chr10-120851134-A-C

Position:

• chr10-120851134-A-C

Variant summary

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

The ENST00000628194.2(WDR11-DT):​n.46T>G 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 0.375 in 516,658 control chromosomes in the GnomAD database, including 37,884 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.35 (9789 hom., cov: 34)
  • Exomes 𝑓: 0.39 (28095 hom.)
• Consequence: WDR11-DT ENST00000628194.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.129

Genes affected

WDR11-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP6: Variant 10-120851134-A-C is Benign according to our data. Variant chr10-120851134-A-C is described in ClinVar as [Benign]. Clinvar id is 1280580.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.46T>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000456120.6	n.11T>G		non_coding_transcript_exon_variant	1/4	5
WDR11-DT	ENST00000598981.5	n.76T>G		non_coding_transcript_exon_variant	1/4	5
WDR11-DT	ENST00000628194.2	n.46T>G		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52717 AN: 152016 Hom.: 9784 Cov.: 34

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.387 AC: 141139 AN: 364524 Hom.: 28095 Cov.: 0 AF XY: 0.384 AC XY: 73534 AN XY: 191376

Gnomad4 AFR exome AF: 0.204

Gnomad4 AMR exome AF: 0.471

Gnomad4 ASJ exome AF: 0.428

Gnomad4 EAS exome AF: 0.362

Gnomad4 SAS exome AF: 0.350

Gnomad4 FIN exome AF: 0.415

Gnomad4 NFE exome AF: 0.396

Gnomad4 OTH exome AF: 0.382

GnomAD4 genome AF: 0.347 AC: 52730 AN: 152134 Hom.: 9789 Cov.: 34 AF XY: 0.348 AC XY: 25879 AN XY: 74362

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.339

Alfa AF: 0.259 Hom.: 1212

Bravo AF: 0.343

Asia WGS AF: 0.356 AC: 1239 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 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.6
DANN	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1659597; hg19: chr10-122610646;