rs11763011

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 0.483 in 151,802 control chromosomes in the GnomAD database, including 18,900 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 0.48 ( 18900 hom., cov: 31)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.73869818A>G intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
73307
AN:
151686
Hom.:
18888
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.297
Gnomad AMI
AF:
0.717
Gnomad AMR
AF:
0.462
Gnomad ASJ
AF:
0.533
Gnomad EAS
AF:
0.439
Gnomad SAS
AF:
0.495
Gnomad FIN
AF:
0.543
Gnomad MID
AF:
0.440
Gnomad NFE
AF:
0.589
Gnomad OTH
AF:
0.482
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73357
AN:
151802
Hom.:
18900
Cov.:
31
AF XY:
0.481
AC XY:
35666
AN XY:
74168
show subpopulations
Gnomad4 AFR
AF:
0.298
Gnomad4 AMR
AF:
0.462
Gnomad4 ASJ
AF:
0.533
Gnomad4 EAS
AF:
0.439
Gnomad4 SAS
AF:
0.496
Gnomad4 FIN
AF:
0.543
Gnomad4 NFE
AF:
0.589
Gnomad4 OTH
AF:
0.476
Alfa
AF:
0.561
Hom.:
19421
Bravo
AF:
0.470
Asia WGS
AF:
0.409
AC:
1427
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.3
DANN
Benign
0.39

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: rs11763011; hg19: chr7-73284148; API