Variant chr11-92988153-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 0.558 in 151,784 control chromosomes in the GnomAD database, including 23,933 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 0.56 ( 23933 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.809

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 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:

0.558

AC:

84573

AN:

151664

Hom.:

23901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.560

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.688

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.516

Gnomad OTH

AF:

0.542

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

GnomAD4 genome

AF:

0.558

AC:

84668

AN:

151784

Hom.:

23933

Cov.:

AF XY:

0.566

AC XY:

41997

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.560

Gnomad4 AMR

AF:

0.658

Gnomad4 ASJ

AF:

0.439

Gnomad4 EAS

AF:

0.694

Gnomad4 SAS

AF:

0.688

Gnomad4 FIN

AF:

0.576

Gnomad4 NFE

AF:

0.516

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.535

Hom.:

10210

Bravo

AF:

0.564

Asia WGS

AF:

0.649

AC:

2253

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.94

DANN

Benign

0.69

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