Variant rs8013053 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 0.824 in 152,186 control chromosomes in the GnomAD database, including 52,794 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 0.82 ( 52794 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.717

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.824

AC:

125261

AN:

152068

Hom.:

52771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.909

Gnomad AMI

AF:

0.802

Gnomad AMR

AF:

0.715

Gnomad ASJ

AF:

0.835

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.757

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.882

Gnomad NFE

AF:

0.844

Gnomad OTH

AF:

0.823

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

GnomAD4 genome

AF:

0.824

AC:

125332

AN:

152186

Hom.:

52794

Cov.:

AF XY:

0.815

AC XY:

60596

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.909

Gnomad4 AMR

AF:

0.715

Gnomad4 ASJ

AF:

0.835

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.756

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.844

Gnomad4 OTH

AF:

0.816

Alfa

AF:

0.830

Hom.:

96844

Bravo

AF:

0.818

Asia WGS

AF:

0.548

AC:

1905

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.38

DANN

Benign

0.44

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