Variant 10-120850879-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000628194.2(WDR11-DT):n.301G>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 0.158 in 159,032 control chromosomes in the GnomAD database, including 2,620 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2457 hom., cov: 33)

Exomes 𝑓: 0.19 ( 163 hom. )

Consequence

WDR11-DT
ENST00000628194.2 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0860

Variant links:

Genes affected

WDR11-DT (HGNC:):

WDR11-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 10-120850879-C-G is Benign according to our data. Variant chr10-120850879-C-G is described in ClinVar as [Benign]. Clinvar id is 1233113.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR11-DT	NR_033850.1 linkuse as main transcript	n.301G>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
WDR11-DT	ENST00000456120.6 linkuse as main transcript	n.266G>C	non_coding_transcript_exon_variant	1/4	5
WDR11-DT	ENST00000628194.2 linkuse as main transcript	n.301G>C	non_coding_transcript_exon_variant	1/3	2
WDR11-DT	ENST00000598981.5 linkuse as main transcript	n.103+228G>C	intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23891

AN:

152158

Hom.:

2456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0505

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.151

GnomAD4 exome

AF:

0.187

AC:

1266

AN:

6756

Hom.:

163

Cov.:

AF XY:

0.188

AC XY:

641

AN XY:

3410

show subpopulations

Gnomad4 AFR exome

AF:

0.0400

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.214

Gnomad4 EAS exome

AF:

0.256

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.0714

Gnomad4 NFE exome

AF:

0.165

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.157

AC:

23884

AN:

152276

Hom.:

2457

Cov.:

AF XY:

0.157

AC XY:

11680

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0503

Gnomad4 AMR

AF:

0.277

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.341

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.184

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.167

Hom.:

327

Bravo

AF:

0.167

Asia WGS

AF:

0.238

AC:

828

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-0.88

CADD

Benign

6.1

DANN

Benign

0.26

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over