Variant rs11026091 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 0.436 in 152,076 control chromosomes in the GnomAD database, including 14,727 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 0.44 ( 14727 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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:

0.436

AC:

66299

AN:

151958

Hom.:

14739

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.505

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.515

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.452

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

GnomAD4 genome

AF:

0.436

AC:

66302

AN:

152076

Hom.:

14727

Cov.:

AF XY:

0.431

AC XY:

32068

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.395

Gnomad4 AMR

AF:

0.363

Gnomad4 ASJ

AF:

0.515

Gnomad4 EAS

AF:

0.628

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.430

Gnomad4 NFE

AF:

0.463

Gnomad4 OTH

AF:

0.453

Alfa

AF:

0.459

Hom.:

32622

Bravo

AF:

0.430

Asia WGS

AF:

0.474

AC:

1649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.3

DANN

Benign

0.66

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