Variant rs2789047 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 0.44 in 151,694 control chromosomes in the GnomAD database, including 17,361 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 0.44 ( 17361 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.329

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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:

0.439

AC:

66568

AN:

151574

Hom.:

17312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.561

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.527

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.435

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

GnomAD4 genome

AF:

0.440

AC:

66682

AN:

151694

Hom.:

17361

Cov.:

AF XY:

0.441

AC XY:

32671

AN XY:

74142

show subpopulations

Gnomad4 AFR

AF:

0.684

Gnomad4 AMR

AF:

0.561

Gnomad4 ASJ

AF:

0.382

Gnomad4 EAS

AF:

0.596

Gnomad4 SAS

AF:

0.527

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.438

Alfa

AF:

0.309

Hom.:

3962

Bravo

AF:

0.476

Asia WGS

AF:

0.584

AC:

2032

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.5

DANN

Benign

0.57

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