Variant rs10447248 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 0.688 in 152,076 control chromosomes in the GnomAD database, including 37,381 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 0.69 ( 37381 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.108580035A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

104563

AN:

151956

Hom.:

37326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.860

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.644

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.656

Gnomad OTH

AF:

0.671

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

GnomAD4 genome

AF:

0.688

AC:

104669

AN:

152076

Hom.:

37381

Cov.:

AF XY:

0.680

AC XY:

50533

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.860

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.315

Gnomad4 SAS

AF:

0.400

Gnomad4 FIN

AF:

0.644

Gnomad4 NFE

AF:

0.656

Gnomad4 OTH

AF:

0.668

Alfa

AF:

0.654

Hom.:

58650

Bravo

AF:

0.694

Asia WGS

AF:

0.420

AC:

1464

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

2.1

DANN

Benign

0.84

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