Variant rs9285235 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 0.497 in 151,932 control chromosomes in the GnomAD database, including 19,191 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 0.50 ( 19191 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.648

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 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:

0.498

AC:

75553

AN:

151814

Hom.:

19183

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.256

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.572

Gnomad OTH

AF:

0.517

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

GnomAD4 genome

AF:

0.497

AC:

75579

AN:

151932

Hom.:

19191

Cov.:

AF XY:

0.489

AC XY:

36310

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.416

Gnomad4 AMR

AF:

0.516

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.388

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.572

Gnomad4 OTH

AF:

0.517

Alfa

AF:

0.385

Hom.:

1031

Bravo

AF:

0.502

Asia WGS

AF:

0.441

AC:

1533

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.0

DANN

Benign

0.49

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