Variant rs1826598 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 0.134 in 152,092 control chromosomes in the GnomAD database, including 1,525 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 0.13 ( 1525 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.414

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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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:

0.134

AC:

20293

AN:

151974

Hom.:

1523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0994

Gnomad FIN

AF:

0.0463

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.134

AC:

20324

AN:

152092

Hom.:

1525

Cov.:

AF XY:

0.133

AC XY:

9860

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.172

Gnomad4 AMR

AF:

0.229

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.105

Gnomad4 SAS

AF:

0.0985

Gnomad4 FIN

AF:

0.0463

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.114

Hom.:

1428

Bravo

AF:

0.151

Asia WGS

AF:

0.117

AC:

408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.48

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