Variant rs684773 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 0.794 in 151,906 control chromosomes in the GnomAD database, including 47,954 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 0.79 ( 47954 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.591

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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:

0.794

AC:

120463

AN:

151788

Hom.:

47900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.804

Gnomad AMI

AF:

0.645

Gnomad AMR

AF:

0.793

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.863

Gnomad SAS

AF:

0.816

Gnomad FIN

AF:

0.863

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.778

Gnomad OTH

AF:

0.770

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

GnomAD4 genome

AF:

0.794

AC:

120579

AN:

151906

Hom.:

47954

Cov.:

AF XY:

0.798

AC XY:

59219

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.804

Gnomad4 AMR

AF:

0.793

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.864

Gnomad4 SAS

AF:

0.815

Gnomad4 FIN

AF:

0.863

Gnomad4 NFE

AF:

0.778

Gnomad4 OTH

AF:

0.772

Alfa

AF:

0.779

Hom.:

23276

Bravo

AF:

0.787

Asia WGS

AF:

0.847

AC:

2944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

DANN

Benign

0.84

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