GeneBe

ENST00000470554.5:n.82-4401C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000470554.5(GSTO1):​n.82-4401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,132 control chromosomes in the GnomAD database, including 5,105 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 0.26 ( 5105 hom., cov: 33)

Consequence

GSTO1
ENST00000470554.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308

Publications

12 publications found
Variant links:
Genes affected
GSTO1 (HGNC:13312): (glutathione S-transferase omega 1) The protein encoded by this gene is an omega class glutathione S-transferase (GST) with glutathione-dependent thiol transferase and dehydroascorbate reductase activities. GSTs are involved in the metabolism of xenobiotics and carcinogens. The encoded protein acts as a homodimer and is found in the cytoplasm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GSTO1ENST00000470554.5 linkn.82-4401C>T intron_variant Intron 1 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.255
AC:
38793
AN:
152014
Hom.:
5105
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.229
Gnomad AMI
AF:
0.205
Gnomad AMR
AF:
0.219
Gnomad ASJ
AF:
0.303
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.255
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.291
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.255
AC:
38815
AN:
152132
Hom.:
5105
Cov.:
33
AF XY:
0.252
AC XY:
18722
AN XY:
74364
show subpopulations
African (AFR)
AF:
0.229
AC:
9513
AN:
41494
American (AMR)
AF:
0.218
AC:
3331
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.303
AC:
1051
AN:
3470
East Asian (EAS)
AF:
0.138
AC:
716
AN:
5182
South Asian (SAS)
AF:
0.182
AC:
878
AN:
4824
European-Finnish (FIN)
AF:
0.255
AC:
2689
AN:
10552
Middle Eastern (MID)
AF:
0.327
AC:
96
AN:
294
European-Non Finnish (NFE)
AF:
0.291
AC:
19788
AN:
68004
Other (OTH)
AF:
0.268
AC:
566
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1498
2995
4493
5990
7488
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
398
796
1194
1592
1990
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.264
Hom.:
811
Bravo
AF:
0.253
Asia WGS
AF:
0.156
AC:
544
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.1
DANN
Benign
0.41
PhyloP100
-0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11191972; hg19: chr10-106007523; API