Variant rs9572903 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.251 in 151,962 control chromosomes in the GnomAD database, including 5,940 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 0.25 ( 5940 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.76

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.21).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.72197576A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38112

AN:

151844

Hom.:

5931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.678

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.255

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

GnomAD4 genome

AF:

0.251

AC:

38144

AN:

151962

Hom.:

5940

Cov.:

AF XY:

0.258

AC XY:

19183

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.331

Gnomad4 ASJ

AF:

0.168

Gnomad4 EAS

AF:

0.678

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.190

Hom.:

3528

Bravo

AF:

0.272

Asia WGS

AF:

0.386

AC:

1343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.21

CADD

Uncertain

DANN

Benign

0.80

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