Variant rs1482308 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 0.272 in 151,856 control chromosomes in the GnomAD database, including 6,105 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 0.27 ( 6105 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.527

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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:

0.273

AC:

41349

AN:

151738

Hom.:

6100

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.281

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

GnomAD4 genome

AF:

0.272

AC:

41370

AN:

151856

Hom.:

6105

Cov.:

AF XY:

0.272

AC XY:

20164

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.315

Gnomad4 OTH

AF:

0.281

Alfa

AF:

0.303

Hom.:

3359

Bravo

AF:

0.268

Asia WGS

AF:

0.352

AC:

1221

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

DANN

Benign

0.67

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