Variant rs2837253 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 0.267 in 152,034 control chromosomes in the GnomAD database, including 6,557 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 0.27 ( 6557 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.420

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.39849329G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40577

AN:

151916

Hom.:

6540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.300

Gnomad OTH

AF:

0.272

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

GnomAD4 genome

AF:

0.267

AC:

40617

AN:

152034

Hom.:

6557

Cov.:

AF XY:

0.274

AC XY:

20339

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.103

Gnomad4 AMR

AF:

0.422

Gnomad4 ASJ

AF:

0.344

Gnomad4 EAS

AF:

0.466

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.300

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.267

Hom.:

2700

Bravo

AF:

0.272

Asia WGS

AF:

0.384

AC:

1335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

DANN

Benign

0.56

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