Variant rs1124933 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 0.437 in 151,744 control chromosomes in the GnomAD database, including 15,413 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 ( 15413 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.115

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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:

0.437

AC:

66291

AN:

151626

Hom.:

15401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.907

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.422

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.420

Gnomad OTH

AF:

0.434

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

GnomAD4 genome

AF:

0.437

AC:

66340

AN:

151744

Hom.:

15413

Cov.:

AF XY:

0.446

AC XY:

33033

AN XY:

74138

show subpopulations

Gnomad4 AFR

AF:

0.362

Gnomad4 AMR

AF:

0.528

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.908

Gnomad4 SAS

AF:

0.631

Gnomad4 FIN

AF:

0.422

Gnomad4 NFE

AF:

0.420

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.430

Hom.:

19732

Bravo

AF:

0.443

Asia WGS

AF:

0.753

AC:

2618

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.0

DANN

Benign

0.37

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