Variant rs12003093 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 0.319 in 152,126 control chromosomes in the GnomAD database, including 9,331 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 0.32 ( 9331 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.218

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 (AFR) allele frequency at 95% confidence interval = 0.537 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:

0.319

AC:

48490

AN:

152008

Hom.:

9283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.542

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.0887

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.274

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

GnomAD4 genome

AF:

0.319

AC:

48596

AN:

152126

Hom.:

9331

Cov.:

AF XY:

0.315

AC XY:

23397

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.543

Gnomad4 AMR

AF:

0.251

Gnomad4 ASJ

AF:

0.297

Gnomad4 EAS

AF:

0.0891

Gnomad4 SAS

AF:

0.220

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.236

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.263

Hom.:

4736

Bravo

AF:

0.327

Asia WGS

AF:

0.161

AC:

561

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

2.0

DANN

Benign

0.65

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