Variant rs7113069 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 0.393 in 138,944 control chromosomes in the GnomAD database, including 11,000 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 0.39 ( 11000 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.59

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 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:

0.393

AC:

54610

AN:

138840

Hom.:

10975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.352

Gnomad AMR

AF:

0.564

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.645

Gnomad SAS

AF:

0.576

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.406

Gnomad NFE

AF:

0.388

Gnomad OTH

AF:

0.422

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

GnomAD4 genome

AF:

0.393

AC:

54646

AN:

138944

Hom.:

11000

Cov.:

AF XY:

0.403

AC XY:

27330

AN XY:

67860

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.565

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.645

Gnomad4 SAS

AF:

0.575

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.388

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.295

Hom.:

1261

Bravo

AF:

0.364

Asia WGS

AF:

0.588

AC:

2039

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.42

DANN

Benign

0.91

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