Variant rs4291477 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 0.446 in 152,028 control chromosomes in the GnomAD database, including 17,119 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 0.45 ( 17119 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.198

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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:

0.446

AC:

67827

AN:

151910

Hom.:

17125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.483

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.808

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.476

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

GnomAD4 genome

AF:

0.446

AC:

67829

AN:

152028

Hom.:

17119

Cov.:

AF XY:

0.449

AC XY:

33397

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.483

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.808

Gnomad4 SAS

AF:

0.451

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.536

Gnomad4 OTH

AF:

0.477

Alfa

AF:

0.514

Hom.:

27685

Bravo

AF:

0.430

Asia WGS

AF:

0.567

AC:

1970

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.65

DANN

Benign

0.78

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