Variant 11-113882290-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 0.504 in 152,112 control chromosomes in the GnomAD database, including 19,883 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 0.50 ( 19883 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.266

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76551

AN:

151994

Hom.:

19847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.579

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.531

Gnomad FIN

AF:

0.460

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.501

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

GnomAD4 genome

AF:

0.504

AC:

76641

AN:

152112

Hom.:

19883

Cov.:

AF XY:

0.508

AC XY:

37741

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.614

Gnomad4 AMR

AF:

0.580

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.621

Gnomad4 SAS

AF:

0.531

Gnomad4 FIN

AF:

0.460

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.506

Alfa

AF:

0.417

Hom.:

5869

Bravo

AF:

0.516

Asia WGS

AF:

0.617

AC:

2144

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.25

DANN

Benign

0.47

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