Variant chr2-232415759-G-A 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 0.214 in 171,222 control chromosomes in the GnomAD database, including 4,857 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 0.21 ( 4240 hom., cov: 33)

Exomes 𝑓: 0.23 ( 617 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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:

0.212

AC:

32178

AN:

152014

Hom.:

4238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0671

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.0971

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.233

GnomAD4 exome

AF:

0.230

AC:

4398

AN:

19090

Hom.:

617

AF XY:

0.235

AC XY:

2382

AN XY:

10156

show subpopulations

Gnomad4 AFR exome

AF:

0.0508

Gnomad4 AMR exome

AF:

0.182

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.0909

Gnomad4 SAS exome

AF:

0.193

Gnomad4 FIN exome

AF:

0.225

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.215

GnomAD4 genome

AF:

0.211

AC:

32170

AN:

152132

Hom.:

4240

Cov.:

AF XY:

0.210

AC XY:

15605

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0669

Gnomad4 AMR

AF:

0.201

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.0967

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.262

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.232

Alfa

AF:

0.241

Hom.:

1095

Bravo

AF:

0.202

Asia WGS

AF:

0.140

AC:

489

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.46

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