Variant chr8-89051573-A-T 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 0.28 in 152,018 control chromosomes in the GnomAD database, including 6,167 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 0.28 ( 6167 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Variant links:

Genome browser will be placed here

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 (SAS) allele frequency at 95% confidence interval = 0.345 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:

0.280

AC:

42594

AN:

151900

Hom.:

6156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.257

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

GnomAD4 genome

AF:

0.280

AC:

42638

AN:

152018

Hom.:

6167

Cov.:

AF XY:

0.282

AC XY:

20973

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.174

Hom.:

358

Bravo

AF:

0.269

Asia WGS

AF:

0.265

AC:

919

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

0.44

DANN

Benign

0.50

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