Variant chr5-58886317-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 0.405 in 152,110 control chromosomes in the GnomAD database, including 13,926 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 0.40 ( 13926 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.120

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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:

0.405

AC:

61505

AN:

151992

Hom.:

13895

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.619

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.344

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

GnomAD4 genome

AF:

0.405

AC:

61583

AN:

152110

Hom.:

13926

Cov.:

AF XY:

0.408

AC XY:

30367

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.599

Gnomad4 AMR

AF:

0.348

Gnomad4 ASJ

AF:

0.278

Gnomad4 EAS

AF:

0.619

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.407

Gnomad4 NFE

AF:

0.295

Gnomad4 OTH

AF:

0.343

Alfa

AF:

0.297

Hom.:

4745

Bravo

AF:

0.409

Asia WGS

AF:

0.490

AC:

1705

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.81

DANN

Benign

0.21

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