Variant rs12682834 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 0.638 in 517,622 control chromosomes in the GnomAD database, including 107,041 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 0.60 ( 27523 hom., cov: 32)

Exomes 𝑓: 0.66 ( 79518 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.561

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 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:

0.596

AC:

90593

AN:

151926

Hom.:

27499

Cov.:

show subpopulations

Gnomad AFR

AF:

0.484

Gnomad AMI

AF:

0.614

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.705

Gnomad SAS

AF:

0.746

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.659

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.614

GnomAD3 exomes

AF:

0.651

AC:

148378

AN:

228042

Hom.:

48885

AF XY:

0.655

AC XY:

82611

AN XY:

126058

show subpopulations

Gnomad AFR exome

AF:

0.472

Gnomad AMR exome

AF:

0.689

Gnomad ASJ exome

AF:

0.733

Gnomad EAS exome

AF:

0.685

Gnomad SAS exome

AF:

0.740

Gnomad FIN exome

AF:

0.591

Gnomad NFE exome

AF:

0.629

Gnomad OTH exome

AF:

0.655

GnomAD4 exome

AF:

0.655

AC:

239570

AN:

365576

Hom.:

79518

Cov.:

AF XY:

0.664

AC XY:

139197

AN XY:

209704

show subpopulations

Gnomad4 AFR exome

AF:

0.475

Gnomad4 AMR exome

AF:

0.688

Gnomad4 ASJ exome

AF:

0.731

Gnomad4 EAS exome

AF:

0.686

Gnomad4 SAS exome

AF:

0.737

Gnomad4 FIN exome

AF:

0.600

Gnomad4 NFE exome

AF:

0.630

Gnomad4 OTH exome

AF:

0.646

GnomAD4 genome

AF:

0.596

AC:

90643

AN:

152046

Hom.:

27523

Cov.:

AF XY:

0.596

AC XY:

44295

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.484

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.735

Gnomad4 EAS

AF:

0.706

Gnomad4 SAS

AF:

0.747

Gnomad4 FIN

AF:

0.583

Gnomad4 NFE

AF:

0.629

Gnomad4 OTH

AF:

0.616

Alfa

AF:

0.634

Hom.:

7025

Bravo

AF:

0.595

Asia WGS

AF:

0.709

AC:

2462

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.38

DANN

Benign

0.28

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