Variant rs2493215 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 0.373 in 152,162 control chromosomes in the GnomAD database, including 11,837 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 0.37 ( 11837 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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:

0.373

AC:

56773

AN:

152044

Hom.:

11837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.412

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.415

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

GnomAD4 genome

AF:

0.373

AC:

56780

AN:

152162

Hom.:

11837

Cov.:

AF XY:

0.376

AC XY:

27960

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.383

Gnomad4 SAS

AF:

0.625

Gnomad4 FIN

AF:

0.412

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.421

Alfa

AF:

0.432

Hom.:

7392

Bravo

AF:

0.355

Asia WGS

AF:

0.472

AC:

1643

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.0

DANN

Benign

0.60

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