Variant rs11941399 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 0.246 in 151,734 control chromosomes in the GnomAD database, including 8,801 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 0.25 ( 8801 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.426

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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:

0.245

AC:

37192

AN:

151620

Hom.:

8760

Cov.:

show subpopulations

Gnomad AFR

AF:

0.590

Gnomad AMI

AF:

0.0231

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.0934

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.0547

Gnomad OTH

AF:

0.226

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

GnomAD4 genome

AF:

0.246

AC:

37285

AN:

151734

Hom.:

8801

Cov.:

AF XY:

0.249

AC XY:

18411

AN XY:

74084

show subpopulations

Gnomad4 AFR

AF:

0.591

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.191

Gnomad4 FIN

AF:

0.0934

Gnomad4 NFE

AF:

0.0547

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.0962

Hom.:

1875

Bravo

AF:

0.273

Asia WGS

AF:

0.354

AC:

1227

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

DANN

Benign

0.42

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