10-120851145-T-C

Position:

• chr10-120851145-T-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.35A>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 0.319 in 536,662 control chromosomes in the GnomAD database, including 28,589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.29 (6872 hom., cov: 34)
  • Exomes 𝑓: 0.33 (21717 hom.)
• Consequence: WDR11-DT ENST00000628194.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0550

Genes affected

WDR11-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 10-120851145-T-C is Benign according to our data. Variant chr10-120851145-T-C is described in ClinVar as [Benign]. Clinvar id is 1261778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.35A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR11-DT	ENST00000598981.5	n.65A>G		non_coding_transcript_exon_variant	1/4	5
WDR11-DT	ENST00000628194.2	n.35A>G		non_coding_transcript_exon_variant	1/3	2
WDR11-DT	ENST00000630905.5	n.313A>G		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43767 AN: 152068 Hom.: 6870 Cov.: 34

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.298

GnomAD4 exome AF: 0.331 AC: 127175 AN: 384476 Hom.: 21717 Cov.: 2 AF XY: 0.330 AC XY: 66597 AN XY: 201624

Gnomad4 AFR exome AF: 0.145

Gnomad4 AMR exome AF: 0.448

Gnomad4 ASJ exome AF: 0.393

Gnomad4 EAS exome AF: 0.365

Gnomad4 SAS exome AF: 0.327

Gnomad4 FIN exome AF: 0.291

Gnomad4 NFE exome AF: 0.330

Gnomad4 OTH exome AF: 0.328

GnomAD4 genome AF: 0.288 AC: 43773 AN: 152186 Hom.: 6872 Cov.: 34 AF XY: 0.288 AC XY: 21394 AN XY: 74400

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.297

Alfa AF: 0.320 Hom.: 7828

Bravo AF: 0.292

Asia WGS AF: 0.342 AC: 1191 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	-0.79
CADD	Benign	7.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11199598; hg19: chr10-122610657;