Variant rs12627387 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 0.275 in 152,256 control chromosomes in the GnomAD database, including 6,908 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 0.28 ( 6903 hom., cov: 33)

Exomes 𝑓: 0.22 ( 5 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41813

AN:

151988

Hom.:

6878

Cov.:

show subpopulations

Gnomad AFR

AF:

0.456

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.270

GnomAD4 exome

AF:

0.220

AC:

AN:

150

Hom.:

AF XY:

0.190

AC XY:

AN XY:

126

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 AMR exome

AF:

0.333

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.400

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.194

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.275

AC:

41897

AN:

152106

Hom.:

6903

Cov.:

AF XY:

0.276

AC XY:

20548

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.457

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.452

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.183

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.0469

Hom.:

Bravo

AF:

0.291

Asia WGS

AF:

0.347

AC:

1206

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.0

DANN

Benign

0.44

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