Variant rs4794888 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 0.529 in 152,090 control chromosomes in the GnomAD database, including 21,553 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 0.53 ( 21553 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.41

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 = 0.673 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:

0.529

AC:

80417

AN:

151972

Hom.:

21535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.584

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.521

Gnomad FIN

AF:

0.598

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.546

Gnomad OTH

AF:

0.540

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

GnomAD4 genome

AF:

0.529

AC:

80479

AN:

152090

Hom.:

21553

Cov.:

AF XY:

0.531

AC XY:

39489

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.478

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.691

Gnomad4 SAS

AF:

0.524

Gnomad4 FIN

AF:

0.598

Gnomad4 NFE

AF:

0.546

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.540

Hom.:

9458

Bravo

AF:

0.519

Asia WGS

AF:

0.577

AC:

2009

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

6.1

DANN

Benign

0.74

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