Variant rs12567614 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 0.495 in 151,998 control chromosomes in the GnomAD database, including 19,644 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 0.50 ( 19644 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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:

0.495

AC:

75238

AN:

151880

Hom.:

19650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.647

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.527

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

GnomAD4 genome

AF:

0.495

AC:

75256

AN:

151998

Hom.:

19644

Cov.:

AF XY:

0.490

AC XY:

36387

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.378

Gnomad4 AMR

AF:

0.484

Gnomad4 ASJ

AF:

0.647

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.542

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.567

Hom.:

49738

Bravo

AF:

0.486

Asia WGS

AF:

0.386

AC:

1341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.11

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