Variant chr8-15884978-G-A 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 0.211 in 152,040 control chromosomes in the GnomAD database, including 3,906 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 0.21 ( 3906 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00800

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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:

0.211

AC:

32046

AN:

151922

Hom.:

3894

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0651

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.0931

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.228

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

GnomAD4 genome

AF:

0.211

AC:

32101

AN:

152040

Hom.:

3906

Cov.:

AF XY:

0.205

AC XY:

15214

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.165

Gnomad4 ASJ

AF:

0.166

Gnomad4 EAS

AF:

0.0651

Gnomad4 SAS

AF:

0.197

Gnomad4 FIN

AF:

0.0931

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.217

Hom.:

549

Bravo

AF:

0.219

Asia WGS

AF:

0.144

AC:

499

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

DANN

Benign

0.40

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