Variant rs9261926 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 0.184 in 134,300 control chromosomes in the GnomAD database, including 2,197 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 0.18 ( 2197 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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:

0.184

AC:

24701

AN:

134180

Hom.:

2197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0397

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.119

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.184

AC:

24716

AN:

134300

Hom.:

2197

Cov.:

AF XY:

0.181

AC XY:

11725

AN XY:

64714

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.134

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.0400

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.172

Alfa

AF:

0.142

Hom.:

1161

Bravo

AF:

0.171

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.2

DANN

Benign

0.49

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