Variant rs12203952 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 0.249 in 151,642 control chromosomes in the GnomAD database, including 4,983 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 0.25 ( 4983 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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:

0.249

AC:

37741

AN:

151522

Hom.:

4970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.261

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.253

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

GnomAD4 genome

AF:

0.249

AC:

37798

AN:

151642

Hom.:

4983

Cov.:

AF XY:

0.253

AC XY:

18720

AN XY:

74100

show subpopulations

Gnomad4 AFR

AF:

0.177

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.261

Gnomad4 EAS

AF:

0.319

Gnomad4 SAS

AF:

0.418

Gnomad4 FIN

AF:

0.212

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.123

Hom.:

195

Bravo

AF:

0.253

Asia WGS

AF:

0.400

AC:

1388

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.8

DANN

Benign

0.63

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