Variant rs1834413 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 151,908 control chromosomes in the GnomAD database, including 27,615 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 ( 27615 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.118

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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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:

89412

AN:

151790

Hom.:

27577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.763

Gnomad AMI

AF:

0.671

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.865

Gnomad SAS

AF:

0.604

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.542

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

GnomAD4 genome

AF:

0.589

AC:

89505

AN:

151908

Hom.:

27615

Cov.:

AF XY:

0.589

AC XY:

43735

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.764

Gnomad4 AMR

AF:

0.491

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.865

Gnomad4 SAS

AF:

0.602

Gnomad4 FIN

AF:

0.513

Gnomad4 NFE

AF:

0.503

Gnomad4 OTH

AF:

0.547

Alfa

AF:

0.511

Hom.:

26927

Bravo

AF:

0.591

Asia WGS

AF:

0.739

AC:

2568

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

3.4

DANN

Benign

0.65

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