Variant rs290258 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 0.181 in 152,020 control chromosomes in the GnomAD database, including 2,747 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 ( 2747 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11

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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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:

0.181

AC:

27475

AN:

151902

Hom.:

2750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.183

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

GnomAD4 genome

AF:

0.181

AC:

27483

AN:

152020

Hom.:

2747

Cov.:

AF XY:

0.184

AC XY:

13705

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.155

Gnomad4 EAS

AF:

0.423

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.251

Gnomad4 NFE

AF:

0.179

Gnomad4 OTH

AF:

0.186

Alfa

AF:

0.177

Hom.:

1014

Bravo

AF:

0.177

Asia WGS

AF:

0.302

AC:

1049

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.93

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