Variant rs9271348 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 0.739 in 151,916 control chromosomes in the GnomAD database, including 41,720 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 0.74 ( 41720 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.946

Variant links:

Genome browser will be placed here

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 (EAS) allele frequency at 95% confidence interval = 0.796 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:

0.739

AC:

112121

AN:

151798

Hom.:

41669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

0.689

Gnomad AMR

AF:

0.802

Gnomad ASJ

AF:

0.803

Gnomad EAS

AF:

0.817

Gnomad SAS

AF:

0.608

Gnomad FIN

AF:

0.816

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.746

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

GnomAD4 genome

AF:

0.739

AC:

112231

AN:

151916

Hom.:

41720

Cov.:

AF XY:

0.742

AC XY:

55105

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.734

Gnomad4 AMR

AF:

0.802

Gnomad4 ASJ

AF:

0.803

Gnomad4 EAS

AF:

0.817

Gnomad4 SAS

AF:

0.610

Gnomad4 FIN

AF:

0.816

Gnomad4 NFE

AF:

0.715

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.730

Hom.:

32753

Bravo

AF:

0.739

Asia WGS

AF:

0.710

AC:

2474

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

6.3

DANN

Benign

0.41

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