Variant rs2489260 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 0.201 in 126,776 control chromosomes in the GnomAD database, including 4,198 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 0.20 ( 4198 hom., cov: 26)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0130

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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:

0.200

AC:

25402

AN:

126720

Hom.:

4170

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.0859

Gnomad MID

AF:

0.208

Gnomad NFE

AF:

0.0789

Gnomad OTH

AF:

0.188

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

GnomAD4 genome

AF:

0.201

AC:

25459

AN:

126776

Hom.:

4198

Cov.:

AF XY:

0.201

AC XY:

12269

AN XY:

61070

show subpopulations

Gnomad4 AFR

AF:

0.459

Gnomad4 AMR

AF:

0.119

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.282

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.0859

Gnomad4 NFE

AF:

0.0789

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.103

Hom.:

2083

Bravo

AF:

0.220

Asia WGS

AF:

0.241

AC:

836

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.9

DANN

Benign

0.54

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