rs12637095

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 0.711 in 151,914 control chromosomes in the GnomAD database, including 39,480 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 0.71 ( 39480 hom., cov: 31)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.118473456T>A intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000243276ENST00000482142.5 linkuse as main transcriptn.232+23167A>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.711
AC:
107932
AN:
151796
Hom.:
39466
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.512
Gnomad AMI
AF:
0.880
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.761
Gnomad EAS
AF:
0.922
Gnomad SAS
AF:
0.819
Gnomad FIN
AF:
0.760
Gnomad MID
AF:
0.813
Gnomad NFE
AF:
0.788
Gnomad OTH
AF:
0.753
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.711
AC:
107994
AN:
151914
Hom.:
39480
Cov.:
31
AF XY:
0.716
AC XY:
53168
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.511
Gnomad4 AMR
AF:
0.741
Gnomad4 ASJ
AF:
0.761
Gnomad4 EAS
AF:
0.922
Gnomad4 SAS
AF:
0.820
Gnomad4 FIN
AF:
0.760
Gnomad4 NFE
AF:
0.788
Gnomad4 OTH
AF:
0.755
Alfa
AF:
0.743
Hom.:
5299
Bravo
AF:
0.701
Asia WGS
AF:
0.828
AC:
2880
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.34
DANN
Benign
0.76

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: rs12637095; hg19: chr3-118192303; API