Variant 11-116567039-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.21 in 151,198 control chromosomes in the GnomAD database, including 6,203 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 6203 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0910

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.116567039C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31719

AN:

151080

Hom.:

6189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.523

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.0858

Gnomad EAS

AF:

0.0774

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0545

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.0925

Gnomad OTH

AF:

0.187

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.210

AC:

31777

AN:

151198

Hom.:

6203

Cov.:

AF XY:

0.203

AC XY:

15001

AN XY:

73854

show subpopulations

Gnomad4 AFR

AF:

0.523

Gnomad4 AMR

AF:

0.113

Gnomad4 ASJ

AF:

0.0858

Gnomad4 EAS

AF:

0.0770

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0545

Gnomad4 NFE

AF:

0.0925

Gnomad4 OTH

AF:

0.187

Alfa

AF:

0.108

Hom.:

1758

Bravo

AF:

0.229

Asia WGS

AF:

0.110

AC:

381

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.6

DANN

Benign

0.57

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over