rs13040307

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 0.19 in 152,126 control chromosomes in the GnomAD database, including 3,275 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 ( 3275 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.46114008C>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.190
AC:
28925
AN:
152008
Hom.:
3269
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0664
Gnomad AMI
AF:
0.351
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.275
Gnomad EAS
AF:
0.286
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.246
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.241
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.190
AC:
28937
AN:
152126
Hom.:
3275
Cov.:
32
AF XY:
0.192
AC XY:
14292
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0665
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.275
Gnomad4 EAS
AF:
0.286
Gnomad4 SAS
AF:
0.311
Gnomad4 FIN
AF:
0.246
Gnomad4 NFE
AF:
0.241
Gnomad4 OTH
AF:
0.190
Alfa
AF:
0.205
Hom.:
668
Bravo
AF:
0.179
Asia WGS
AF:
0.240
AC:
837
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.34

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: rs13040307; hg19: chr20-44742647; API