Variant 8-86801493-CTA-CTATA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.252 in 151,756 control chromosomes in the GnomAD database, including 5,237 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5237 hom., cov: 22)

Consequence

intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.719

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.86801493_86801494insTA		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253778	ENST00000520649.1 linkuse as main transcript	n.450-13741_450-13740insTA		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38173

AN:

151638

Hom.:

5246

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.00386

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.288

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

GnomAD4 genome

AF:

0.252

AC:

38176

AN:

151756

Hom.:

5237

Cov.:

AF XY:

0.246

AC XY:

18220

AN XY:

74162

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.241

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.00386

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.286

Alfa

AF:

0.269

Hom.:

695

Bravo

AF:

0.251

Asia WGS

AF:

0.122

AC:

426

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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