Variant rs11239177 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 0.469 in 152,014 control chromosomes in the GnomAD database, including 16,930 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 0.47 ( 16930 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.102

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=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71193

AN:

151894

Hom.:

16900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.459

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

GnomAD4 genome

AF:

0.469

AC:

71284

AN:

152014

Hom.:

16930

Cov.:

AF XY:

0.468

AC XY:

34765

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.473

Gnomad4 AMR

AF:

0.505

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.474

Gnomad4 FIN

AF:

0.485

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.463

Alfa

AF:

0.460

Hom.:

32325

Bravo

AF:

0.475

Asia WGS

AF:

0.439

AC:

1527

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.2

DANN

Benign

0.89

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