Variant rs12870000 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 0.24 in 152,012 control chromosomes in the GnomAD database, including 4,456 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 0.24 ( 4456 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.382

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 = 0.313 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:

0.240

AC:

36442

AN:

151894

Hom.:

4449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.240

AC:

36477

AN:

152012

Hom.:

4456

Cov.:

AF XY:

0.242

AC XY:

17986

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.325

Gnomad4 SAS

AF:

0.188

Gnomad4 FIN

AF:

0.321

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.237

Hom.:

6178

Bravo

AF:

0.237

Asia WGS

AF:

0.221

AC:

769

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.82

DANN

Benign

0.81

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