Variant rs6069551 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 0.309 in 151,412 control chromosomes in the GnomAD database, including 8,411 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 0.31 ( 8411 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.319

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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46713

AN:

151294

Hom.:

8390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.493

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.226

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.264

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

GnomAD4 genome

AF:

0.309

AC:

46775

AN:

151412

Hom.:

8411

Cov.:

AF XY:

0.309

AC XY:

22826

AN XY:

73940

show subpopulations

Gnomad4 AFR

AF:

0.493

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.160

Gnomad4 EAS

AF:

0.468

Gnomad4 SAS

AF:

0.297

Gnomad4 FIN

AF:

0.280

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.239

Hom.:

3585

Bravo

AF:

0.314

Asia WGS

AF:

0.426

AC:

1481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

DANN

Benign

0.65

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