Variant rs9275572 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 0.59 in 151,908 control chromosomes in the GnomAD database, including 26,819 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 0.59 ( 26819 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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:

0.590

AC:

89567

AN:

151788

Hom.:

26811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.562

Gnomad AMI

AF:

0.730

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.754

Gnomad EAS

AF:

0.731

Gnomad SAS

AF:

0.668

Gnomad FIN

AF:

0.543

Gnomad MID

AF:

0.694

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.639

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

GnomAD4 genome

AF:

0.590

AC:

89624

AN:

151908

Hom.:

26819

Cov.:

AF XY:

0.590

AC XY:

43819

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.562

Gnomad4 AMR

AF:

0.643

Gnomad4 ASJ

AF:

0.754

Gnomad4 EAS

AF:

0.730

Gnomad4 SAS

AF:

0.667

Gnomad4 FIN

AF:

0.543

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.641

Alfa

AF:

0.588

Hom.:

28122

Asia WGS

AF:

0.718

AC:

2496

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.4

DANN

Benign

0.57

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