Menu
GeneBe

rs4646903

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 0.184 in 150878 control chromosomes in the gnomAD Genomes database, including 3337 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 0.18 ( 3337 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.929

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=-0.91).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.184
AC:
27781
AN:
150878
Hom.:
3337
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.239
Gnomad AMI
AF:
0.120
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.123
Gnomad EAS
AF:
0.415
Gnomad SAS
AF:
0.324
Gnomad FIN
AF:
0.128
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.101
Gnomad OTH
AF:
0.190
Alfa
AF:
0.137
Hom.:
244
Bravo
AF:
0.200
Asia WGS
AF:
0.417
AC:
1448
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
3.5
Dann
Benign
0.46

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.

Other links and lift over

dbSNP: rs4646903; hg19: chr15-75011641; API