Variant 11-113385608-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 0.373 in 152,084 control chromosomes in the GnomAD database, including 12,811 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 0.37 ( 12811 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.110

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 (NFE) allele frequency at 95% confidence interval = 0.515 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:

0.373

AC:

56720

AN:

151966

Hom.:

12824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.521

Gnomad EAS

AF:

0.0562

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.430

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

GnomAD4 genome

AF:

0.373

AC:

56713

AN:

152084

Hom.:

12811

Cov.:

AF XY:

0.366

AC XY:

27185

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.155

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.521

Gnomad4 EAS

AF:

0.0557

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.439

Gnomad4 NFE

AF:

0.519

Gnomad4 OTH

AF:

0.427

Alfa

AF:

0.323

Hom.:

1181

Bravo

AF:

0.354

Asia WGS

AF:

0.201

AC:

700

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

2.9

DANN

Benign

0.44

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