Variant rs3129889 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 0.906 in 152,218 control chromosomes in the GnomAD database, including 62,668 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 0.91 ( 62668 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

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 = 0.974 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:

0.906

AC:

137815

AN:

152100

Hom.:

62615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.953

Gnomad AMI

AF:

0.913

Gnomad AMR

AF:

0.928

Gnomad ASJ

AF:

0.978

Gnomad EAS

AF:

0.996

Gnomad SAS

AF:

0.980

Gnomad FIN

AF:

0.871

Gnomad MID

AF:

0.946

Gnomad NFE

AF:

0.861

Gnomad OTH

AF:

0.932

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

GnomAD4 genome

AF:

0.906

AC:

137926

AN:

152218

Hom.:

62668

Cov.:

AF XY:

0.908

AC XY:

67543

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.953

Gnomad4 AMR

AF:

0.928

Gnomad4 ASJ

AF:

0.978

Gnomad4 EAS

AF:

0.996

Gnomad4 SAS

AF:

0.981

Gnomad4 FIN

AF:

0.871

Gnomad4 NFE

AF:

0.861

Gnomad4 OTH

AF:

0.933

Alfa

AF:

0.881

Hom.:

85322

Bravo

AF:

0.913

Asia WGS

AF:

0.982

AC:

3414

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

0.24

DANN

Benign

0.27

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