Variant rs10894294 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 0.569 in 151,850 control chromosomes in the GnomAD database, including 25,492 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 0.57 ( 25492 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.130960853C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.569

AC:

86262

AN:

151732

Hom.:

25457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

0.428

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.539

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.540

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

GnomAD4 genome

AF:

0.569

AC:

86354

AN:

151850

Hom.:

25492

Cov.:

AF XY:

0.565

AC XY:

41906

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.735

Gnomad4 AMR

AF:

0.493

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.538

Gnomad4 SAS

AF:

0.596

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.533

Hom.:

6634

Bravo

AF:

0.578

Asia WGS

AF:

0.609

AC:

2120

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.22

DANN

Benign

0.15

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