Variant rs4371699 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 151,992 control chromosomes in the GnomAD database, including 55,872 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 ( 55872 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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:

129832

AN:

151874

Hom.:

55804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.933

Gnomad AMI

AF:

0.789

Gnomad AMR

AF:

0.867

Gnomad ASJ

AF:

0.829

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.905

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.780

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.834

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

GnomAD4 genome

AF:

0.855

AC:

129958

AN:

151992

Hom.:

55872

Cov.:

AF XY:

0.856

AC XY:

63590

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.933

Gnomad4 AMR

AF:

0.867

Gnomad4 ASJ

AF:

0.829

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.905

Gnomad4 FIN

AF:

0.775

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.836

Alfa

AF:

0.812

Hom.:

62095

Bravo

AF:

0.863

Asia WGS

AF:

0.922

AC:

3200

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.1

DANN

Benign

0.42

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