Variant chr8-109228745-T-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 0.638 in 152,126 control chromosomes in the GnomAD database, including 32,421 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 0.64 ( 32421 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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:

0.637

AC:

96896

AN:

152008

Hom.:

32368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.846

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.528

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.623

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

GnomAD4 genome

AF:

0.638

AC:

97011

AN:

152126

Hom.:

32421

Cov.:

AF XY:

0.637

AC XY:

47332

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.846

Gnomad4 AMR

AF:

0.656

Gnomad4 ASJ

AF:

0.403

Gnomad4 EAS

AF:

0.528

Gnomad4 SAS

AF:

0.668

Gnomad4 FIN

AF:

0.522

Gnomad4 NFE

AF:

0.542

Gnomad4 OTH

AF:

0.626

Alfa

AF:

0.470

Hom.:

1374

Bravo

AF:

0.653

Asia WGS

AF:

0.658

AC:

2289

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.2

DANN

Benign

0.66

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