rs13361189

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 0.207 in 151,828 control chromosomes in the GnomAD database, including 5,212 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 0.21 ( 5212 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.790
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.206
AC:
31327
AN:
151710
Hom.:
5198
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.442
Gnomad AMI
AF:
0.0351
Gnomad AMR
AF:
0.155
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.432
Gnomad SAS
AF:
0.211
Gnomad FIN
AF:
0.0818
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.0819
Gnomad OTH
AF:
0.210
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.207
AC:
31378
AN:
151828
Hom.:
5212
Cov.:
32
AF XY:
0.207
AC XY:
15330
AN XY:
74190
show subpopulations
Gnomad4 AFR
AF:
0.442
Gnomad4 AMR
AF:
0.154
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.433
Gnomad4 SAS
AF:
0.210
Gnomad4 FIN
AF:
0.0818
Gnomad4 NFE
AF:
0.0819
Gnomad4 OTH
AF:
0.211
Alfa
AF:
0.125
Hom.:
2008
Bravo
AF:
0.224
Asia WGS
AF:
0.322
AC:
1122
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.93
DANN
Benign
0.38

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: rs13361189; hg19: chr5-150223387; COSMIC: COSV72988837; API