22-23960293-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PP5_ModerateBS2_Supporting

The NM_001080843.4(GSTT2B):​c.200+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000303 in 1,611,566 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).

Frequency

Genomes: 𝑓 0.00038 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00030 ( 9 hom. )

Consequence

GSTT2B
NM_001080843.4 splice_donor, intron

Scores

1
6
Splicing: ADA: 1.000
2

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 3.12
Variant links:
Genes affected
GSTT2B (HGNC:33437): (glutathione S-transferase theta 2B) The protein encoded by this gene, glutathione S-transferase (GST) theta 2B (GSTT2B), is a member of a superfamily of proteins that catalyze the conjugation of reduced glutathione to a variety of electrophilic and hydrophobic compounds. Human GSTs can be divided into five main classes: alpha, mu, pi, theta, and zeta. The theta class includes GSTT1, GSTT2, and GSTT2B. GSTT2 and GSTT2B are nearly identical to each other, and share 55% amino acid identity with GSTT1. All three genes may play a role in human carcinogenesis. The GSTT2B gene is a pseudogene in some populations. [provided by RefSeq, Sep 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PP5
Variant 22-23960293-C-T is Pathogenic according to our data. Variant chr22-23960293-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3064991.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 9 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GSTT2BNM_001080843.4 linkc.200+1G>A splice_donor_variant, intron_variant Intron 2 of 4 ENST00000290765.9 NP_001074312.1 P0CG30G9J6Q5
GSTT2BNM_001363804.1 linkc.200+1G>A splice_donor_variant, intron_variant Intron 2 of 4 NP_001350733.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GSTT2BENST00000290765.9 linkc.200+1G>A splice_donor_variant, intron_variant Intron 2 of 4 1 NM_001080843.4 ENSP00000290765.4 P0CG30
GSTT2BENST00000404172.3 linkc.200+1G>A splice_donor_variant, intron_variant Intron 2 of 4 1 ENSP00000385116.3 Q6ICJ4
ENSG00000290199ENST00000703580.1 linkn.309+13475G>A intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.000370
AC:
56
AN:
151320
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000727
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.000132
Gnomad ASJ
AF:
0.00609
Gnomad EAS
AF:
0.000392
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000281
Gnomad OTH
AF:
0.000482
GnomAD4 exome
AF:
0.000295
AC:
431
AN:
1460138
Hom.:
9
Cov.:
32
AF XY:
0.000332
AC XY:
241
AN XY:
726408
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.000157
Gnomad4 ASJ exome
AF:
0.00649
Gnomad4 EAS exome
AF:
0.000202
Gnomad4 SAS exome
AF:
0.000534
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.000131
Gnomad4 OTH exome
AF:
0.000680
GnomAD4 genome
AF:
0.000376
AC:
57
AN:
151428
Hom.:
0
Cov.:
30
AF XY:
0.000297
AC XY:
22
AN XY:
74032
show subpopulations
Gnomad4 AFR
AF:
0.0000966
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00609
Gnomad4 EAS
AF:
0.000393
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000281
Gnomad4 OTH
AF:
0.000477
Alfa
AF:
0.00358
Hom.:
2
ExAC
AF:
0.00641
AC:
86

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Megalencephalic leukoencephalopathy with subcortical cysts 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingGenomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research CentreMar 25, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.010
T
BayesDel_noAF
Benign
-0.25
CADD
Uncertain
25
DANN
Benign
0.96
Eigen
Uncertain
0.50
Eigen_PC
Benign
0.18
FATHMM_MKL
Benign
0.71
D
GERP RS
1.8

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.88
SpliceAI score (max)
0.99
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.54
Position offset: 23
DS_DL_spliceai
0.99
Position offset: 1

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: rs181983734; hg19: chr22-24302480; COSMIC: COSV51960313; COSMIC: COSV51960313; API