Variant rs12589063 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 0.579 in 151,964 control chromosomes in the GnomAD database, including 25,611 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 0.58 ( 25611 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358

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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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:

0.579

AC:

87886

AN:

151846

Hom.:

25575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.590

Gnomad AMI

AF:

0.627

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.635

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.580

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

GnomAD4 genome

AF:

0.579

AC:

87969

AN:

151964

Hom.:

25611

Cov.:

AF XY:

0.576

AC XY:

42798

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.591

Gnomad4 AMR

AF:

0.500

Gnomad4 ASJ

AF:

0.551

Gnomad4 EAS

AF:

0.482

Gnomad4 SAS

AF:

0.517

Gnomad4 FIN

AF:

0.635

Gnomad4 NFE

AF:

0.594

Gnomad4 OTH

AF:

0.580

Alfa

AF:

0.581

Hom.:

42267

Bravo

AF:

0.568

Asia WGS

AF:

0.544

AC:

1889

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

DANN

Benign

0.41

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