Variant rs2724041 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.642 in 152,006 control chromosomes in the GnomAD database, including 32,207 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 0.64 ( 32207 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.67

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.96447615G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97457

AN:

151888

Hom.:

32159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.775

Gnomad AMI

AF:

0.686

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.648

Gnomad EAS

AF:

0.873

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.546

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.555

Gnomad OTH

AF:

0.675

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

GnomAD4 genome

AF:

0.642

AC:

97562

AN:

152006

Hom.:

32207

Cov.:

AF XY:

0.642

AC XY:

47715

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.776

Gnomad4 AMR

AF:

0.655

Gnomad4 ASJ

AF:

0.648

Gnomad4 EAS

AF:

0.873

Gnomad4 SAS

AF:

0.601

Gnomad4 FIN

AF:

0.546

Gnomad4 NFE

AF:

0.555

Gnomad4 OTH

AF:

0.680

Alfa

AF:

0.577

Hom.:

51915

Bravo

AF:

0.660

Asia WGS

AF:

0.774

AC:

2689

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.60

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