Variant 12-25840870-T-C 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 0.189 in 151,818 control chromosomes in the GnomAD database, including 2,775 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 0.19 ( 2775 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.855

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 = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28732

AN:

151702

Hom.:

2777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.121

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.190

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

GnomAD4 genome

AF:

0.189

AC:

28734

AN:

151818

Hom.:

2775

Cov.:

AF XY:

0.187

AC XY:

13898

AN XY:

74174

show subpopulations

Gnomad4 AFR

AF:

0.214

Gnomad4 AMR

AF:

0.143

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.121

Gnomad4 SAS

AF:

0.219

Gnomad4 FIN

AF:

0.190

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.187

Alfa

AF:

0.188

Hom.:

4282

Bravo

AF:

0.187

Asia WGS

AF:

0.183

AC:

640

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

5.1

DANN

Benign

0.65

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