Variant chr11-13150680-G-A 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 0.423 in 151,730 control chromosomes in the GnomAD database, including 13,826 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 0.42 ( 13826 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0660

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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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:

0.423

AC:

64201

AN:

151612

Hom.:

13830

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.441

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.439

Gnomad OTH

AF:

0.426

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

GnomAD4 genome

AF:

0.423

AC:

64228

AN:

151730

Hom.:

13826

Cov.:

AF XY:

0.430

AC XY:

31895

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.347

Gnomad4 AMR

AF:

0.429

Gnomad4 ASJ

AF:

0.489

Gnomad4 EAS

AF:

0.566

Gnomad4 SAS

AF:

0.600

Gnomad4 FIN

AF:

0.441

Gnomad4 NFE

AF:

0.439

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.438

Hom.:

10476

Bravo

AF:

0.412

Asia WGS

AF:

0.581

AC:

2019

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.8

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