Variant rs27348 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 0.239 in 151,790 control chromosomes in the GnomAD database, including 4,580 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 ( 4580 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.219

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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:

0.239

AC:

36199

AN:

151672

Hom.:

4568

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.224

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

GnomAD4 genome

AF:

0.239

AC:

36237

AN:

151790

Hom.:

4580

Cov.:

AF XY:

0.245

AC XY:

18184

AN XY:

74162

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.212

Gnomad4 ASJ

AF:

0.272

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.239

Hom.:

545

Bravo

AF:

0.230

Asia WGS

AF:

0.387

AC:

1345

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.1

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