Variant rs9351730 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 0.418 in 151,876 control chromosomes in the GnomAD database, including 14,995 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 0.42 ( 14995 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.172

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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:

0.418

AC:

63482

AN:

151762

Hom.:

14969

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.463

Gnomad EAS

AF:

0.843

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.419

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

GnomAD4 genome

AF:

0.418

AC:

63533

AN:

151876

Hom.:

14995

Cov.:

AF XY:

0.426

AC XY:

31596

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.546

Gnomad4 ASJ

AF:

0.463

Gnomad4 EAS

AF:

0.843

Gnomad4 SAS

AF:

0.602

Gnomad4 FIN

AF:

0.452

Gnomad4 NFE

AF:

0.465

Gnomad4 OTH

AF:

0.424

Alfa

AF:

0.458

Hom.:

8276

Bravo

AF:

0.418

Asia WGS

AF:

0.702

AC:

2431

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.7

DANN

Benign

0.73

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