Variant rs12987465 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 0.407 in 151,718 control chromosomes in the GnomAD database, including 13,324 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 0.41 ( 13324 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.485

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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:

0.407

AC:

61755

AN:

151600

Hom.:

13311

Cov.:

show subpopulations

Gnomad AFR

AF:

0.537

Gnomad AMI

AF:

0.375

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.521

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.408

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

GnomAD4 genome

AF:

0.407

AC:

61790

AN:

151718

Hom.:

13324

Cov.:

AF XY:

0.410

AC XY:

30410

AN XY:

74136

show subpopulations

Gnomad4 AFR

AF:

0.537

Gnomad4 AMR

AF:

0.447

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.521

Gnomad4 SAS

AF:

0.391

Gnomad4 FIN

AF:

0.353

Gnomad4 NFE

AF:

0.325

Gnomad4 OTH

AF:

0.404

Alfa

AF:

0.337

Hom.:

19782

Bravo

AF:

0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.24

DANN

Benign

0.34

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