Variant rs2870784 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 0.773 in 152,174 control chromosomes in the GnomAD database, including 46,266 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 0.77 ( 46266 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.686

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.66088600A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.773

AC:

117502

AN:

152056

Hom.:

46217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.910

Gnomad AMI

AF:

0.811

Gnomad AMR

AF:

0.630

Gnomad ASJ

AF:

0.805

Gnomad EAS

AF:

0.892

Gnomad SAS

AF:

0.756

Gnomad FIN

AF:

0.708

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.722

Gnomad OTH

AF:

0.748

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

GnomAD4 genome

AF:

0.773

AC:

117609

AN:

152174

Hom.:

46266

Cov.:

AF XY:

0.771

AC XY:

57391

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.910

Gnomad4 AMR

AF:

0.630

Gnomad4 ASJ

AF:

0.805

Gnomad4 EAS

AF:

0.892

Gnomad4 SAS

AF:

0.756

Gnomad4 FIN

AF:

0.708

Gnomad4 NFE

AF:

0.722

Gnomad4 OTH

AF:

0.745

Alfa

AF:

0.691

Hom.:

6905

Bravo

AF:

0.771

Asia WGS

AF:

0.812

AC:

2823

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

DANN

Benign

0.53

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