Variant rs17526697 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 0.0657 in 152,382 control chromosomes in the GnomAD database, including 416 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 0.066 ( 416 hom., cov: 32)

Exomes 𝑓: 0.077 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.207

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 = 0.0967 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0658

AC:

10002

AN:

152068

Hom.:

417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0175

Gnomad AMI

AF:

0.0549

Gnomad AMR

AF:

0.0642

Gnomad ASJ

AF:

0.0732

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0816

Gnomad FIN

AF:

0.0652

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0987

Gnomad OTH

AF:

0.0755

GnomAD4 exome

AF:

0.0765

AC:

AN:

196

Hom.:

AF XY:

0.0672

AC XY:

AN XY:

134

show subpopulations

Gnomad4 FIN exome

AF:

0.0773

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0657

AC:

9994

AN:

152186

Hom.:

416

Cov.:

AF XY:

0.0640

AC XY:

4762

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0174

Gnomad4 AMR

AF:

0.0641

Gnomad4 ASJ

AF:

0.0732

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0821

Gnomad4 FIN

AF:

0.0652

Gnomad4 NFE

AF:

0.0987

Gnomad4 OTH

AF:

0.0743

Alfa

AF:

0.0935

Hom.:

985

Bravo

AF:

0.0631

Asia WGS

AF:

0.0300

AC:

108

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

0.80

DANN

Benign

0.50

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