Variant rs2842026 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 0.417 in 151,932 control chromosomes in the GnomAD database, including 14,248 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 0.42 ( 14248 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.938

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.163063299A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63405

AN:

151812

Hom.:

14258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.328

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.412

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

GnomAD4 genome

AF:

0.417

AC:

63401

AN:

151932

Hom.:

14248

Cov.:

AF XY:

0.417

AC XY:

30971

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.478

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.496

Gnomad4 SAS

AF:

0.327

Gnomad4 FIN

AF:

0.534

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.411

Alfa

AF:

0.303

Hom.:

814

Bravo

AF:

0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.8

DANN

Benign

0.81

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