Variant rs17340555 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 0.0688 in 152,794 control chromosomes in the GnomAD database, including 504 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 0.069 ( 503 hom., cov: 33)

Exomes 𝑓: 0.12 ( 1 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.88

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.098 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:

0.0687

AC:

10464

AN:

152224

Hom.:

503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0172

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0587

Gnomad ASJ

AF:

0.0781

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0205

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.0598

GnomAD4 exome

AF:

0.124

AC:

AN:

452

Hom.:

AF XY:

0.109

AC XY:

AN XY:

274

show subpopulations

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.222

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0687

AC:

10461

AN:

152342

Hom.:

503

Cov.:

AF XY:

0.0696

AC XY:

5184

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.0171

Gnomad4 AMR

AF:

0.0585

Gnomad4 ASJ

AF:

0.0781

Gnomad4 EAS

AF:

0.000770

Gnomad4 SAS

AF:

0.0207

Gnomad4 FIN

AF:

0.143

Gnomad4 NFE

AF:

0.100

Gnomad4 OTH

AF:

0.0591

Alfa

AF:

0.0906

Hom.:

944

Bravo

AF:

0.0609

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

Cadd

Benign

0.098

Dann

Benign

0.20

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