Variant rs10147986 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 0.749 in 151,724 control chromosomes in the GnomAD database, including 42,929 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 0.75 ( 42929 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

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=-1.12).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.51756077A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259111	ENST00000557308.1 linkuse as main transcript	n.216-5030A>C		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113534

AN:

151602

Hom.:

42896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.742

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.712

Gnomad EAS

AF:

0.995

Gnomad SAS

AF:

0.744

Gnomad FIN

AF:

0.810

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.758

Gnomad OTH

AF:

0.749

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

GnomAD4 genome

AF:

0.749

AC:

113624

AN:

151724

Hom.:

42929

Cov.:

AF XY:

0.757

AC XY:

56159

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.664

Gnomad4 AMR

AF:

0.821

Gnomad4 ASJ

AF:

0.712

Gnomad4 EAS

AF:

0.995

Gnomad4 SAS

AF:

0.742

Gnomad4 FIN

AF:

0.810

Gnomad4 NFE

AF:

0.758

Gnomad4 OTH

AF:

0.751

Alfa

AF:

0.720

Hom.:

3342

Bravo

AF:

0.751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.82

DANN

Benign

0.085

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