Variant rs2873892 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 0.242 in 151,900 control chromosomes in the GnomAD database, including 4,997 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 0.24 ( 4997 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36718

AN:

151782

Hom.:

4988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.231

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

GnomAD4 genome

AF:

0.242

AC:

36736

AN:

151900

Hom.:

4997

Cov.:

AF XY:

0.246

AC XY:

18236

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.377

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.204

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.311

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.139

Hom.:

267

Bravo

AF:

0.243

Asia WGS

AF:

0.177

AC:

617

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.55

DANN

Benign

0.78

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