Menu
GeneBe

rs3851179

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 0.691 in 152,074 control chromosomes in the GnomAD database, including 37,006 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 0.69 ( 37006 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.482
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 (AFR) allele frequency at 95% confidence interval = 0.837 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:
0.691
AC:
104974
AN:
151956
Hom.:
36969
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.845
Gnomad AMI
AF:
0.521
Gnomad AMR
AF:
0.638
Gnomad ASJ
AF:
0.606
Gnomad EAS
AF:
0.603
Gnomad SAS
AF:
0.610
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.635
Gnomad OTH
AF:
0.682
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.691
AC:
105069
AN:
152074
Hom.:
37006
Cov.:
32
AF XY:
0.688
AC XY:
51121
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.845
Gnomad4 AMR
AF:
0.637
Gnomad4 ASJ
AF:
0.606
Gnomad4 EAS
AF:
0.602
Gnomad4 SAS
AF:
0.612
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.635
Gnomad4 OTH
AF:
0.682
Alfa
AF:
0.639
Hom.:
68346
Bravo
AF:
0.696
Asia WGS
AF:
0.602
AC:
2093
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
3.8
Dann
Benign
0.73

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: rs3851179; hg19: chr11-85868640; API