Variant rs17523519 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.398 in 151,772 control chromosomes in the GnomAD database, including 13,725 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 13724 hom., cov: 0)

Exomes 𝑓: 0.24 ( 1 hom. )

Consequence

intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.224

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.44345008delC		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.397

AC:

60243

AN:

151584

Hom.:

13684

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.895

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.276

Gnomad OTH

AF:

0.366

GnomAD4 exome

AF:

0.243

AC:

AN:

Hom.:

AF XY:

0.227

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.233

GnomAD4 genome

AF:

0.398

AC:

60339

AN:

151702

Hom.:

13724

Cov.:

AF XY:

0.409

AC XY:

30313

AN XY:

74126

show subpopulations

Gnomad4 AFR

AF:

0.528

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.895

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.276

Gnomad4 OTH

AF:

0.374

Alfa

AF:

0.332

Hom.:

1120

Bravo

AF:

0.409

Asia WGS

AF:

0.690

AC:

2398

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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