Variant 11-13150176-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The variant allele was found at a frequency of 0.118 in 152,010 control chromosomes in the GnomAD database, including 3,268 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 0.12 ( 3268 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.543

Variant links:

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ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.12).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17897

AN:

151892

Hom.:

3250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0671

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.0598

Gnomad SAS

AF:

0.00725

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00238

Gnomad OTH

AF:

0.100

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

GnomAD4 genome

AF:

0.118

AC:

17963

AN:

152010

Hom.:

3268

Cov.:

AF XY:

0.114

AC XY:

8506

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.391

Gnomad4 AMR

AF:

0.0674

Gnomad4 ASJ

AF:

0.0159

Gnomad4 EAS

AF:

0.0595

Gnomad4 SAS

AF:

0.00705

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00237

Gnomad4 OTH

AF:

0.0997

Alfa

AF:

0.0165

Hom.:

220

Bravo

AF:

0.138

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.12

CADD

Benign

DANN

Benign

0.74

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