Variant 12-53239847-A-T 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 0.6 in 151,760 control chromosomes in the GnomAD database, including 27,816 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 0.60 ( 27816 hom., cov: 30)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.57

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.53239847A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91034

AN:

151640

Hom.:

27780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.650

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.801

Gnomad SAS

AF:

0.748

Gnomad FIN

AF:

0.531

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.600

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

GnomAD4 genome

AF:

0.600

AC:

91128

AN:

151760

Hom.:

27816

Cov.:

AF XY:

0.602

AC XY:

44632

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.650

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.551

Gnomad4 EAS

AF:

0.802

Gnomad4 SAS

AF:

0.748

Gnomad4 FIN

AF:

0.531

Gnomad4 NFE

AF:

0.556

Gnomad4 OTH

AF:

0.605

Alfa

AF:

0.571

Hom.:

2949

Bravo

AF:

0.609

Asia WGS

AF:

0.734

AC:

2552

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.037

DANN

Benign

0.31

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