Variant rs17725099 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 0.243 in 151,832 control chromosomes in the GnomAD database, including 4,548 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 0.24 ( 4548 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.273 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:

0.243

AC:

36897

AN:

151714

Hom.:

4546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.239

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

GnomAD4 genome

AF:

0.243

AC:

36909

AN:

151832

Hom.:

4548

Cov.:

AF XY:

0.241

AC XY:

17892

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.286

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.238

Alfa

AF:

0.247

Hom.:

7811

Bravo

AF:

0.237

Asia WGS

AF:

0.267

AC:

931

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.96

DANN

Benign

0.45

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