Variant rs12515012 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 0.401 in 152,022 control chromosomes in the GnomAD database, including 12,479 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 0.40 ( 12479 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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:

0.401

AC:

60890

AN:

151904

Hom.:

12454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.439

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.408

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

GnomAD4 genome

AF:

0.401

AC:

60937

AN:

152022

Hom.:

12479

Cov.:

AF XY:

0.406

AC XY:

30169

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.449

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.504

Gnomad4 SAS

AF:

0.499

Gnomad4 FIN

AF:

0.395

Gnomad4 NFE

AF:

0.399

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.406

Hom.:

1572

Bravo

AF:

0.402

Asia WGS

AF:

0.510

AC:

1773

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.3

DANN

Benign

0.17

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