Variant rs915854 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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 0.62 ( 30352 hom., cov: 20)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0910

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.43046656C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.620

AC:

81027

AN:

130636

Hom.:

30329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.608

Gnomad ASJ

AF:

0.523

Gnomad EAS

AF:

0.718

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.600

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

GnomAD4 genome

AF:

0.620

AC:

81098

AN:

130754

Hom.:

30352

Cov.:

AF XY:

0.621

AC XY:

39085

AN XY:

62982

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.608

Gnomad4 ASJ

AF:

0.523

Gnomad4 EAS

AF:

0.719

Gnomad4 SAS

AF:

0.622

Gnomad4 FIN

AF:

0.628

Gnomad4 NFE

AF:

0.622

Gnomad4 OTH

AF:

0.598

Alfa

AF:

0.568

Hom.:

3188

Asia WGS

AF:

0.534

AC:

1857

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.1

DANN

Benign

0.38

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