rs12111385

Positions:

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 0.238 in 148,170 control chromosomes in the GnomAD database, including 4,253 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 0.24 ( 4253 hom., cov: 27)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91
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=-1.1).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.8370534T>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000285216ENST00000644718.1 linkuse as main transcriptn.560+62974T>C intron_variant
ENSG00000234763ENST00000651914.1 linkuse as main transcriptn.160-2118A>G intron_variant
ENSG00000234763ENST00000655767.1 linkuse as main transcriptn.229-7702A>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.238
AC:
35247
AN:
148080
Hom.:
4251
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.213
Gnomad AMI
AF:
0.117
Gnomad AMR
AF:
0.244
Gnomad ASJ
AF:
0.281
Gnomad EAS
AF:
0.0932
Gnomad SAS
AF:
0.212
Gnomad FIN
AF:
0.210
Gnomad MID
AF:
0.235
Gnomad NFE
AF:
0.267
Gnomad OTH
AF:
0.253
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.238
AC:
35266
AN:
148170
Hom.:
4253
Cov.:
27
AF XY:
0.232
AC XY:
16738
AN XY:
72018
show subpopulations
Gnomad4 AFR
AF:
0.213
Gnomad4 AMR
AF:
0.244
Gnomad4 ASJ
AF:
0.281
Gnomad4 EAS
AF:
0.0930
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.210
Gnomad4 NFE
AF:
0.267
Gnomad4 OTH
AF:
0.251
Alfa
AF:
0.252
Hom.:
619
Bravo
AF:
0.236
Asia WGS
AF:
0.144
AC:
504
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.12
DANN
Benign
0.15

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: rs12111385; hg19: chr6-8370767; API