Variant rs12313946 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 0.367 in 151,346 control chromosomes in the GnomAD database, including 10,367 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 0.37 ( 10367 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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:

0.367

AC:

55553

AN:

151238

Hom.:

10363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.338

Gnomad AMI

AF:

0.393

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.505

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.372

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.353

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

GnomAD4 genome

AF:

0.367

AC:

55573

AN:

151346

Hom.:

10367

Cov.:

AF XY:

0.371

AC XY:

27385

AN XY:

73912

show subpopulations

Gnomad4 AFR

AF:

0.338

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.414

Gnomad4 EAS

AF:

0.506

Gnomad4 SAS

AF:

0.485

Gnomad4 FIN

AF:

0.410

Gnomad4 NFE

AF:

0.369

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.373

Hom.:

24692

Bravo

AF:

0.359

Asia WGS

AF:

0.462

AC:

1608

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.51

DANN

Benign

0.56

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