Variant rs9285426 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 0.426 in 152,006 control chromosomes in the GnomAD database, including 15,240 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 0.43 ( 15240 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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:

0.427

AC:

64824

AN:

151888

Hom.:

15244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.655

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.625

Gnomad FIN

AF:

0.653

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.436

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

GnomAD4 genome

AF:

0.426

AC:

64827

AN:

152006

Hom.:

15240

Cov.:

AF XY:

0.436

AC XY:

32358

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.254

Gnomad4 AMR

AF:

0.409

Gnomad4 ASJ

AF:

0.405

Gnomad4 EAS

AF:

0.220

Gnomad4 SAS

AF:

0.625

Gnomad4 FIN

AF:

0.653

Gnomad4 NFE

AF:

0.500

Gnomad4 OTH

AF:

0.433

Alfa

AF:

0.461

Hom.:

5188

Bravo

AF:

0.394

Asia WGS

AF:

0.415

AC:

1444

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.55

DANN

Benign

0.61

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