Variant rs12457996 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 0.188 in 152,036 control chromosomes in the GnomAD database, including 2,898 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 0.19 ( 2898 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.125

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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:

0.188

AC:

28617

AN:

151918

Hom.:

2892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.00580

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.200

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

GnomAD4 genome

AF:

0.188

AC:

28640

AN:

152036

Hom.:

2898

Cov.:

AF XY:

0.187

AC XY:

13893

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.00581

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.226

Gnomad4 OTH

AF:

0.196

Alfa

AF:

0.214

Hom.:

5771

Bravo

AF:

0.184

Asia WGS

AF:

0.0700

AC:

244

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

DANN

Benign

0.66

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