Variant rs9552733 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 0.375 in 151,968 control chromosomes in the GnomAD database, including 11,426 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 0.38 ( 11426 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.244

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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:

0.375

AC:

56988

AN:

151850

Hom.:

11427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.515

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.443

Gnomad OTH

AF:

0.383

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

GnomAD4 genome

AF:

0.375

AC:

57012

AN:

151968

Hom.:

11426

Cov.:

AF XY:

0.377

AC XY:

27965

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.516

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.443

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.391

Hom.:

8091

Bravo

AF:

0.355

Asia WGS

AF:

0.389

AC:

1355

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.6

DANN

Benign

0.64

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