Variant rs4681173 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.115 in 152,232 control chromosomes in the GnomAD database, including 1,838 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 0.11 ( 1838 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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:

0.115

AC:

17451

AN:

152114

Hom.:

1832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0421

Gnomad AMI

AF:

0.0791

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.0932

Gnomad EAS

AF:

0.534

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.115

AC:

17475

AN:

152232

Hom.:

1838

Cov.:

AF XY:

0.122

AC XY:

9090

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0423

Gnomad4 AMR

AF:

0.148

Gnomad4 ASJ

AF:

0.0932

Gnomad4 EAS

AF:

0.533

Gnomad4 SAS

AF:

0.389

Gnomad4 FIN

AF:

0.119

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.115

Hom.:

2825

Bravo

AF:

0.111

Asia WGS

AF:

0.456

AC:

1580

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.83

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