Variant 12-52537683-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 0.495 in 152,076 control chromosomes in the GnomAD database, including 20,290 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 0.49 ( 20290 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 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:

0.494

AC:

75106

AN:

151958

Hom.:

20242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.714

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.500

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.416

Gnomad OTH

AF:

0.486

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

GnomAD4 genome

AF:

0.495

AC:

75212

AN:

152076

Hom.:

20290

Cov.:

AF XY:

0.493

AC XY:

36677

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.715

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.500

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.416

Gnomad4 OTH

AF:

0.481

Alfa

AF:

0.427

Hom.:

18861

Bravo

AF:

0.502

Asia WGS

AF:

0.356

AC:

1240

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.1

DANN

Benign

0.73

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