Variant rs3741834 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 0.0298 in 152,298 control chromosomes in the GnomAD database, including 243 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 0.030 ( 243 hom., cov: 32)

Exomes 𝑓: 0.071 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.45

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=-0.58).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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:

0.0298

AC:

4539

AN:

152124

Hom.:

244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0109

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0394

Gnomad ASJ

AF:

0.0184

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.0903

Gnomad FIN

AF:

0.0198

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0197

Gnomad OTH

AF:

0.0321

GnomAD4 exome

AF:

0.0714

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0952

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0238

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.0298

AC:

4535

AN:

152242

Hom.:

243

Cov.:

AF XY:

0.0329

AC XY:

2450

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0110

Gnomad4 AMR

AF:

0.0393

Gnomad4 ASJ

AF:

0.0184

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.0906

Gnomad4 FIN

AF:

0.0198

Gnomad4 NFE

AF:

0.0197

Gnomad4 OTH

AF:

0.0313

Alfa

AF:

0.0210

Hom.:

Bravo

AF:

0.0309

Asia WGS

AF:

0.166

AC:

576

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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