Variant rs12725332 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 0.152 in 151,496 control chromosomes in the GnomAD database, including 2,139 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 0.15 ( 2139 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.248

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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:

0.152

AC:

23076

AN:

151380

Hom.:

2136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0417

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.152

AC:

23074

AN:

151496

Hom.:

2139

Cov.:

AF XY:

0.153

AC XY:

11293

AN XY:

74002

show subpopulations

Gnomad4 AFR

AF:

0.0417

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.0806

Gnomad4 EAS

AF:

0.236

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.185

Hom.:

5496

Bravo

AF:

0.150

Asia WGS

AF:

0.176

AC:

607

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.065

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