Variant 8-59255330-T-G 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 0.453 in 151,746 control chromosomes in the GnomAD database, including 16,024 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 0.45 ( 16024 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.10

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 (AMR) allele frequency at 95% confidence interval = 0.588 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:

0.453

AC:

68647

AN:

151626

Hom.:

16002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.408

Gnomad AMI

AF:

0.716

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.535

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.505

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

GnomAD4 genome

AF:

0.453

AC:

68721

AN:

151746

Hom.:

16024

Cov.:

AF XY:

0.450

AC XY:

33387

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.409

Gnomad4 AMR

AF:

0.598

Gnomad4 ASJ

AF:

0.438

Gnomad4 EAS

AF:

0.535

Gnomad4 SAS

AF:

0.303

Gnomad4 FIN

AF:

0.375

Gnomad4 NFE

AF:

0.459

Gnomad4 OTH

AF:

0.503

Alfa

AF:

0.451

Hom.:

1927

Bravo

AF:

0.478

Asia WGS

AF:

0.406

AC:

1410

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.77

DANN

Benign

0.28

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