Variant rs12702919 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 0.545 in 151,222 control chromosomes in the GnomAD database, including 23,002 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 0.55 ( 23002 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75

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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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:

0.545

AC:

82370

AN:

151100

Hom.:

22985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.514

Gnomad ASJ

AF:

0.575

Gnomad EAS

AF:

0.842

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.680

Gnomad MID

AF:

0.599

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.567

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

GnomAD4 genome

AF:

0.545

AC:

82430

AN:

151222

Hom.:

23002

Cov.:

AF XY:

0.551

AC XY:

40711

AN XY:

73874

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.514

Gnomad4 ASJ

AF:

0.575

Gnomad4 EAS

AF:

0.843

Gnomad4 SAS

AF:

0.510

Gnomad4 FIN

AF:

0.680

Gnomad4 NFE

AF:

0.560

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.555

Hom.:

3016

Bravo

AF:

0.535

Asia WGS

AF:

0.685

AC:

2356

AN:

3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.25

DANN

Benign

0.73

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