Variant rs2018498 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 0.516 in 143,184 control chromosomes in the GnomAD database, including 26,098 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 0.52 ( 26098 hom., cov: 28)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340

Variant links:

Genome browser will be placed here

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 (EAS) allele frequency at 95% confidence interval = 0.925 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:

0.516

AC:

73797

AN:

143066

Hom.:

26054

Cov.:

show subpopulations

Gnomad AFR

AF:

0.758

Gnomad AMI

AF:

0.445

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.948

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.406

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.473

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

GnomAD4 genome

AF:

0.516

AC:

73898

AN:

143184

Hom.:

26098

Cov.:

AF XY:

0.520

AC XY:

36218

AN XY:

69714

show subpopulations

Gnomad4 AFR

AF:

0.758

Gnomad4 AMR

AF:

0.500

Gnomad4 ASJ

AF:

0.423

Gnomad4 EAS

AF:

0.948

Gnomad4 SAS

AF:

0.640

Gnomad4 FIN

AF:

0.319

Gnomad4 NFE

AF:

0.361

Gnomad4 OTH

AF:

0.482

Alfa

AF:

0.486

Hom.:

4108

Asia WGS

AF:

0.796

AC:

2669

AN:

3360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.3

DANN

Benign

0.51

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