Variant rs12545625 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 0.236 in 152,092 control chromosomes in the GnomAD database, including 4,463 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 0.24 ( 4463 hom., cov: 33)

Exomes 𝑓: 0.18 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.201

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=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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:

0.236

AC:

35888

AN:

151936

Hom.:

4462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.256

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.167

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.184

AC:

AN:

Hom.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.236

AC:

35914

AN:

152054

Hom.:

4463

Cov.:

AF XY:

0.237

AC XY:

17640

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.112

Gnomad4 SAS

AF:

0.168

Gnomad4 FIN

AF:

0.307

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.249

Hom.:

2387

Bravo

AF:

0.228

Asia WGS

AF:

0.147

AC:

512

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

DANN

Benign

0.24

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