Variant rs4456603 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 0.855 in 151,896 control chromosomes in the GnomAD database, including 56,129 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 0.86 ( 56129 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.30

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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:

0.855

AC:

129806

AN:

151778

Hom.:

56102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.730

Gnomad AMI

AF:

0.962

Gnomad AMR

AF:

0.852

Gnomad ASJ

AF:

0.869

Gnomad EAS

AF:

0.844

Gnomad SAS

AF:

0.866

Gnomad FIN

AF:

0.882

Gnomad MID

AF:

0.818

Gnomad NFE

AF:

0.927

Gnomad OTH

AF:

0.835

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

GnomAD4 genome

AF:

0.855

AC:

129882

AN:

151896

Hom.:

56129

Cov.:

AF XY:

0.851

AC XY:

63180

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.730

Gnomad4 AMR

AF:

0.852

Gnomad4 ASJ

AF:

0.869

Gnomad4 EAS

AF:

0.844

Gnomad4 SAS

AF:

0.866

Gnomad4 FIN

AF:

0.882

Gnomad4 NFE

AF:

0.927

Gnomad4 OTH

AF:

0.837

Alfa

AF:

0.903

Hom.:

84976

Bravo

AF:

0.847

Asia WGS

AF:

0.848

AC:

2951

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.12

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