10-120851127-T-G

Position:

• chr10-120851127-T-G

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.53A>C 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 0.136 in 505,340 control chromosomes in the GnomAD database, including 5,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.13 (1318 hom., cov: 33)
  • Exomes 𝑓: 0.14 (3847 hom.)
• Consequence: WDR11-DT ENST00000628194.2 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=-0.59).
• BP6: Variant 10-120851127-T-G is Benign according to our data. Variant chr10-120851127-T-G is described in ClinVar as [Benign]. Clinvar id is 1289331.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11-DT	NR_033850.1	n.53A>C		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.18A>C		non_coding_transcript_exon_variant	1/4	5
WDR11-DT	ENST00000598981.5	n.83A>C		non_coding_transcript_exon_variant	1/4	5
WDR11-DT	ENST00000628194.2	n.53A>C		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19294 AN: 152150 Hom.: 1315 Cov.: 33

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.140 AC: 49393 AN: 353072 Hom.: 3847 Cov.: 0 AF XY: 0.141 AC XY: 26243 AN XY: 185656

Gnomad4 AFR exome AF: 0.0813

Gnomad4 AMR exome AF: 0.104

Gnomad4 ASJ exome AF: 0.164

Gnomad4 EAS exome AF: 0.0251

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.149

Gnomad4 OTH exome AF: 0.144

GnomAD4 genome AF: 0.127 AC: 19303 AN: 152268 Hom.: 1318 Cov.: 33 AF XY: 0.127 AC XY: 9441 AN XY: 74442

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.141

Alfa AF: 0.134 Hom.: 1008

Bravo AF: 0.120

Asia WGS AF: 0.100 AC: 347 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	-0.59
CADD	Benign	5.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12778011; hg19: chr10-122610639;