Variant rs282802 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 0.715 in 152,160 control chromosomes in the GnomAD database, including 39,110 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 0.72 ( 39110 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.614

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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:

0.715

AC:

108721

AN:

152042

Hom.:

39069

Cov.:

show subpopulations

Gnomad AFR

AF:

0.686

Gnomad AMI

AF:

0.545

Gnomad AMR

AF:

0.690

Gnomad ASJ

AF:

0.708

Gnomad EAS

AF:

0.836

Gnomad SAS

AF:

0.777

Gnomad FIN

AF:

0.722

Gnomad MID

AF:

0.747

Gnomad NFE

AF:

0.726

Gnomad OTH

AF:

0.725

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

GnomAD4 genome

AF:

0.715

AC:

108816

AN:

152160

Hom.:

39110

Cov.:

AF XY:

0.717

AC XY:

53327

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.686

Gnomad4 AMR

AF:

0.689

Gnomad4 ASJ

AF:

0.708

Gnomad4 EAS

AF:

0.836

Gnomad4 SAS

AF:

0.779

Gnomad4 FIN

AF:

0.722

Gnomad4 NFE

AF:

0.726

Gnomad4 OTH

AF:

0.726

Alfa

AF:

0.723

Hom.:

81733

Bravo

AF:

0.708

Asia WGS

AF:

0.794

AC:

2759

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

1.4

DANN

Benign

0.82

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