Variant rs11126185 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 0.589 in 151,810 control chromosomes in the GnomAD database, including 27,893 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 0.59 ( 27893 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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:

0.589

AC:

89361

AN:

151694

Hom.:

27879

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.730

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.892

Gnomad SAS

AF:

0.698

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.653

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

GnomAD4 genome

AF:

0.589

AC:

89401

AN:

151810

Hom.:

27893

Cov.:

AF XY:

0.594

AC XY:

44094

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.731

Gnomad4 ASJ

AF:

0.747

Gnomad4 EAS

AF:

0.892

Gnomad4 SAS

AF:

0.700

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.637

Gnomad4 OTH

AF:

0.656

Alfa

AF:

0.649

Hom.:

62088

Bravo

AF:

0.589

Asia WGS

AF:

0.791

AC:

2751

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.84

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