Variant rs2427393 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 0.226 in 161,680 control chromosomes in the GnomAD database, including 4,281 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 0.23 ( 4062 hom., cov: 34)

Exomes 𝑓: 0.21 ( 219 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

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=-1.08).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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:

0.227

AC:

34450

AN:

152092

Hom.:

4061

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.208

Gnomad OTH

AF:

0.220

GnomAD4 exome

AF:

0.213

AC:

2014

AN:

9470

Hom.:

219

AF XY:

0.216

AC XY:

1007

AN XY:

4660

show subpopulations

Gnomad4 AFR exome

AF:

0.203

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.274

Gnomad4 FIN exome

AF:

0.215

Gnomad4 NFE exome

AF:

0.239

Gnomad4 OTH exome

AF:

0.214

GnomAD4 genome

AF:

0.226

AC:

34454

AN:

152210

Hom.:

4062

Cov.:

AF XY:

0.226

AC XY:

16838

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.208

Gnomad4 OTH

AF:

0.216

Alfa

AF:

0.207

Hom.:

3571

Bravo

AF:

0.223

Asia WGS

AF:

0.237

AC:

826

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.68

DANN

Benign

0.57

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