Variant rs2457221 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 0.462 in 151,932 control chromosomes in the GnomAD database, including 16,436 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 0.46 ( 16436 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.870

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=-0.97).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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:

0.462

AC:

70195

AN:

151814

Hom.:

16433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.324

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.478

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.464

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

GnomAD4 genome

AF:

0.462

AC:

70227

AN:

151932

Hom.:

16436

Cov.:

AF XY:

0.461

AC XY:

34214

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.450

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.542

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.466

Alfa

AF:

0.464

Hom.:

3322

Bravo

AF:

0.457

Asia WGS

AF:

0.489

AC:

1708

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.19

DANN

Benign

0.37

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