Variant rs2516463 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 0.107 in 151,916 control chromosomes in the GnomAD database, including 1,318 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 0.11 ( 1318 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.316

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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:

0.107

AC:

16177

AN:

151798

Hom.:

1315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.0838

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.0858

Gnomad FIN

AF:

0.0119

Gnomad MID

AF:

0.105

Gnomad NFE

AF:

0.0745

Gnomad OTH

AF:

0.137

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

GnomAD4 genome

AF:

0.107

AC:

16196

AN:

151916

Hom.:

1318

Cov.:

AF XY:

0.104

AC XY:

7692

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.0838

Gnomad4 EAS

AF:

0.0102

Gnomad4 SAS

AF:

0.0859

Gnomad4 FIN

AF:

0.0119

Gnomad4 NFE

AF:

0.0745

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.0699

Hom.:

291

Bravo

AF:

0.121

Asia WGS

AF:

0.0630

AC:

219

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

4.2

DANN

Benign

0.47

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