Menu
GeneBe

rs13394027

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 0.187 in 152,080 control chromosomes in the GnomAD database, including 3,425 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 0.19 ( 3425 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 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:
0.187
AC:
28421
AN:
151962
Hom.:
3414
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0468
Gnomad AMI
AF:
0.185
Gnomad AMR
AF:
0.221
Gnomad ASJ
AF:
0.205
Gnomad EAS
AF:
0.454
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.255
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.223
Gnomad OTH
AF:
0.215
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.187
AC:
28428
AN:
152080
Hom.:
3425
Cov.:
33
AF XY:
0.193
AC XY:
14321
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0466
Gnomad4 AMR
AF:
0.222
Gnomad4 ASJ
AF:
0.205
Gnomad4 EAS
AF:
0.454
Gnomad4 SAS
AF:
0.307
Gnomad4 FIN
AF:
0.255
Gnomad4 NFE
AF:
0.223
Gnomad4 OTH
AF:
0.224
Alfa
AF:
0.220
Hom.:
4258
Bravo
AF:
0.175
Asia WGS
AF:
0.376
AC:
1306
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.10
DANN
Benign
0.89

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: rs13394027; hg19: chr2-20882056; API