Variant rs11830829 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 0.432 in 151,934 control chromosomes in the GnomAD database, including 15,734 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 0.43 ( 15734 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.942

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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:

0.432

AC:

65519

AN:

151816

Hom.:

15701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.718

Gnomad SAS

AF:

0.423

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.416

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

GnomAD4 genome

AF:

0.432

AC:

65616

AN:

151934

Hom.:

15734

Cov.:

AF XY:

0.433

AC XY:

32147

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.384

Gnomad4 ASJ

AF:

0.249

Gnomad4 EAS

AF:

0.716

Gnomad4 SAS

AF:

0.424

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.419

Alfa

AF:

0.339

Hom.:

17798

Bravo

AF:

0.445

Asia WGS

AF:

0.563

AC:

1956

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.30

DANN

Benign

0.52

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