XM_024452202.2:c.472-3540G>T

Variant summary

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

The XM_024452202.2(GSTT4):​c.472-3540G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 144,176 control chromosomes in the GnomAD database, including 16,062 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 0.50 ( 16062 hom., cov: 28)

Consequence

GSTT4
XM_024452202.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.620

Publications

13 publications found
Variant links:
Genes affected
GSTT4 (HGNC:26930): (glutathione S-transferase theta 4) Predicted to enable glutathione transferase activity. Predicted to be involved in glutathione metabolic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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 (Cadd=6.259).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GSTT4XM_024452202.2 linkc.472-3540G>T intron_variant Intron 3 of 3 XP_024307970.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.496
AC:
71519
AN:
144058
Hom.:
16059
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.331
Gnomad AMI
AF:
0.696
Gnomad AMR
AF:
0.570
Gnomad ASJ
AF:
0.522
Gnomad EAS
AF:
0.368
Gnomad SAS
AF:
0.608
Gnomad FIN
AF:
0.579
Gnomad MID
AF:
0.586
Gnomad NFE
AF:
0.565
Gnomad OTH
AF:
0.514
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.496
AC:
71540
AN:
144176
Hom.:
16062
Cov.:
28
AF XY:
0.503
AC XY:
35315
AN XY:
70234
show subpopulations
African (AFR)
AF:
0.330
AC:
12953
AN:
39202
American (AMR)
AF:
0.571
AC:
8173
AN:
14320
Ashkenazi Jewish (ASJ)
AF:
0.522
AC:
1743
AN:
3336
East Asian (EAS)
AF:
0.367
AC:
1815
AN:
4940
South Asian (SAS)
AF:
0.608
AC:
2709
AN:
4458
European-Finnish (FIN)
AF:
0.579
AC:
5723
AN:
9882
Middle Eastern (MID)
AF:
0.571
AC:
160
AN:
280
European-Non Finnish (NFE)
AF:
0.565
AC:
36644
AN:
64896
Other (OTH)
AF:
0.511
AC:
1030
AN:
2014
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.519
Heterozygous variant carriers
0
1480
2960
4441
5921
7401
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
674
1348
2022
2696
3370
<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:
0.524
Hom.:
5106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
CADD
Benign
6.3
PhyloP100
0.62

Splicing

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

Publications

Other links and lift over

dbSNP: rs5760147; hg19: -; API