Variant rs13028485 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 0.0805 in 152,202 control chromosomes in the GnomAD database, including 548 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 0.080 ( 548 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

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 (EAS) allele frequency at 95% confidence interval = 0.188 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:

0.0804

AC:

12221

AN:

152082

Hom.:

546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0925

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0822

Gnomad ASJ

AF:

0.0694

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0470

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0680

Gnomad OTH

AF:

0.0796

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

GnomAD4 genome

AF:

0.0805

AC:

12246

AN:

152202

Hom.:

548

Cov.:

AF XY:

0.0809

AC XY:

6018

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0926

Gnomad4 AMR

AF:

0.0824

Gnomad4 ASJ

AF:

0.0694

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.0470

Gnomad4 NFE

AF:

0.0680

Gnomad4 OTH

AF:

0.0806

Alfa

AF:

0.0726

Hom.:

556

Bravo

AF:

0.0821

Asia WGS

AF:

0.153

AC:

531

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

4.8

DANN

Benign

0.70

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