Variant rs9939524 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 0.199 in 456,426 control chromosomes in the GnomAD database, including 11,337 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 0.22 ( 4844 hom., cov: 32)

Exomes 𝑓: 0.19 ( 6493 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.453

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.57689840A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260467	ENST00000563062.1 linkuse as main transcript	n.464-3020T>C		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34084

AN:

151940

Hom.:

4826

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.0850

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.202

GnomAD3 exomes

AF:

0.211

AC:

28842

AN:

136984

Hom.:

3784

AF XY:

0.207

AC XY:

15424

AN XY:

74482

show subpopulations

Gnomad AFR exome

AF:

0.381

Gnomad AMR exome

AF:

0.326

Gnomad ASJ exome

AF:

0.0971

Gnomad EAS exome

AF:

0.328

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.107

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.186

AC:

56560

AN:

304368

Hom.:

6493

Cov.:

AF XY:

0.190

AC XY:

32848

AN XY:

173318

show subpopulations

Gnomad4 AFR exome

AF:

0.373

Gnomad4 AMR exome

AF:

0.324

Gnomad4 ASJ exome

AF:

0.0962

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.249

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.225

AC:

34151

AN:

152058

Hom.:

4844

Cov.:

AF XY:

0.227

AC XY:

16899

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.286

Gnomad4 ASJ

AF:

0.0850

Gnomad4 EAS

AF:

0.328

Gnomad4 SAS

AF:

0.247

Gnomad4 FIN

AF:

0.102

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.205

Alfa

AF:

0.153

Hom.:

2618

Bravo

AF:

0.246

Asia WGS

AF:

0.271

AC:

942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.3

DANN

Uncertain

0.99

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