Variant rs3020176 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 0.659 in 151,840 control chromosomes in the GnomAD database, including 33,210 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 0.66 ( 33210 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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:

0.659

AC:

99978

AN:

151722

Hom.:

33155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.707

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.731

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.817

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.681

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.605

Gnomad OTH

AF:

0.636

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

GnomAD4 genome

AF:

0.659

AC:

100082

AN:

151840

Hom.:

33210

Cov.:

AF XY:

0.667

AC XY:

49490

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.708

Gnomad4 AMR

AF:

0.731

Gnomad4 ASJ

AF:

0.517

Gnomad4 EAS

AF:

0.817

Gnomad4 SAS

AF:

0.688

Gnomad4 FIN

AF:

0.681

Gnomad4 NFE

AF:

0.605

Gnomad4 OTH

AF:

0.635

Alfa

AF:

0.606

Hom.:

12463

Bravo

AF:

0.664

Asia WGS

AF:

0.725

AC:

2519

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.025

DANN

Benign

0.46

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