Variant 8-58500365-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The variant allele was found at a frequency of 0.568 in 407,118 control chromosomes in the GnomAD database, including 66,983 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.55 ( 23418 hom., cov: 32)

Exomes 𝑓: 0.58 ( 43565 hom. )

Consequence

Unknown

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.25

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=-0.29).

BP6

Variant 8-58500365-G-T is Benign according to our data. Variant chr8-58500365-G-T is described in ClinVar as [Benign]. Clinvar id is 1229509.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 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:

0.548

AC:

83111

AN:

151748

Hom.:

23399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.663

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.537

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.666

Gnomad NFE

AF:

0.601

Gnomad OTH

AF:

0.567

GnomAD4 exome

AF:

0.581

AC:

148203

AN:

255252

Hom.:

43565

AF XY:

0.578

AC XY:

78587

AN XY:

135926

show subpopulations

Gnomad4 AFR exome

AF:

0.411

Gnomad4 AMR exome

AF:

0.683

Gnomad4 ASJ exome

AF:

0.644

Gnomad4 EAS exome

AF:

0.519

Gnomad4 SAS exome

AF:

0.551

Gnomad4 FIN exome

AF:

0.519

Gnomad4 NFE exome

AF:

0.596

Gnomad4 OTH exome

AF:

0.589

GnomAD4 genome

AF:

0.548

AC:

83159

AN:

151866

Hom.:

23418

Cov.:

AF XY:

0.545

AC XY:

40441

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.419

Gnomad4 AMR

AF:

0.663

Gnomad4 ASJ

AF:

0.654

Gnomad4 EAS

AF:

0.538

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.488

Gnomad4 NFE

AF:

0.601

Gnomad4 OTH

AF:

0.573

Alfa

AF:

0.593

Hom.:

41179

Bravo

AF:

0.555

Asia WGS

AF:

0.559

AC:

1945

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 29, 2018

This variant is associated with the following publications: (PMID: 15262185, 19850125, 18178499, 18728290, 20884100) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

DANN

Benign

0.85

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over