rs2110483

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 0.178 in 151,956 control chromosomes in the GnomAD database, including 4,592 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 0.18 ( 4592 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.938
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.94250781T>C intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.177
AC:
26929
AN:
151838
Hom.:
4573
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.450
Gnomad AMI
AF:
0.107
Gnomad AMR
AF:
0.155
Gnomad ASJ
AF:
0.0870
Gnomad EAS
AF:
0.0455
Gnomad SAS
AF:
0.0723
Gnomad FIN
AF:
0.0270
Gnomad MID
AF:
0.153
Gnomad NFE
AF:
0.0637
Gnomad OTH
AF:
0.164
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.178
AC:
26994
AN:
151956
Hom.:
4592
Cov.:
32
AF XY:
0.172
AC XY:
12748
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.451
Gnomad4 AMR
AF:
0.155
Gnomad4 ASJ
AF:
0.0870
Gnomad4 EAS
AF:
0.0455
Gnomad4 SAS
AF:
0.0726
Gnomad4 FIN
AF:
0.0270
Gnomad4 NFE
AF:
0.0637
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.134
Hom.:
692
Bravo
AF:
0.202
Asia WGS
AF:
0.0970
AC:
339
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.55
DANN
Benign
0.45

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: rs2110483; hg19: chr7-93880093; API