Variant rs9399032 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.372 in 152,032 control chromosomes in the GnomAD database, including 11,397 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 0.37 ( 11397 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.15

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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:

0.372

AC:

56457

AN:

151914

Hom.:

11378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.790

Gnomad SAS

AF:

0.423

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.375

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

GnomAD4 genome

AF:

0.372

AC:

56511

AN:

152032

Hom.:

11397

Cov.:

AF XY:

0.374

AC XY:

27766

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.328

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.790

Gnomad4 SAS

AF:

0.422

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.324

Gnomad4 OTH

AF:

0.380

Alfa

AF:

0.351

Hom.:

1236

Bravo

AF:

0.381

Asia WGS

AF:

0.619

AC:

2149

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.89

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