Variant rs928413 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 0.682 in 151,794 control chromosomes in the GnomAD database, including 36,468 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 0.68 ( 36468 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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:

0.682

AC:

103459

AN:

151676

Hom.:

36453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.627

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.670

Gnomad EAS

AF:

0.933

Gnomad SAS

AF:

0.761

Gnomad FIN

AF:

0.740

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.744

Gnomad OTH

AF:

0.695

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

GnomAD4 genome

AF:

0.682

AC:

103516

AN:

151794

Hom.:

36468

Cov.:

AF XY:

0.684

AC XY:

50721

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.761

Gnomad4 ASJ

AF:

0.670

Gnomad4 EAS

AF:

0.934

Gnomad4 SAS

AF:

0.761

Gnomad4 FIN

AF:

0.740

Gnomad4 NFE

AF:

0.744

Gnomad4 OTH

AF:

0.694

Alfa

AF:

0.717

Hom.:

16490

Bravo

AF:

0.672

Asia WGS

AF:

0.806

AC:

2802

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.48

DANN

Benign

0.45

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