Variant rs927821 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 0.849 in 152,058 control chromosomes in the GnomAD database, including 54,990 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 0.85 ( 54990 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.862

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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 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:

0.849

AC:

129015

AN:

151940

Hom.:

54939

Cov.:

show subpopulations

Gnomad AFR

AF:

0.913

Gnomad AMI

AF:

0.925

Gnomad AMR

AF:

0.861

Gnomad ASJ

AF:

0.763

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.914

Gnomad FIN

AF:

0.805

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.817

Gnomad OTH

AF:

0.833

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

GnomAD4 genome

AF:

0.849

AC:

129125

AN:

152058

Hom.:

54990

Cov.:

AF XY:

0.850

AC XY:

63185

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.912

Gnomad4 AMR

AF:

0.861

Gnomad4 ASJ

AF:

0.763

Gnomad4 EAS

AF:

0.813

Gnomad4 SAS

AF:

0.915

Gnomad4 FIN

AF:

0.805

Gnomad4 NFE

AF:

0.817

Gnomad4 OTH

AF:

0.829

Alfa

AF:

0.824

Hom.:

81936

Bravo

AF:

0.856

Asia WGS

AF:

0.877

AC:

3049

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

DANN

Benign

0.87

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