Genetic Variant GSTT2B:c.352-15C>G (chr22-23958473-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001080843.4(GSTT2B):c.352-15C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 ( 27330 hom., cov: 36)

Exomes 𝑓: 0.65 ( 271116 hom. )

Failed GnomAD Quality Control

Consequence

GSTT2B
NM_001080843.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.474

Publications

7 publications found

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]

GSTT2B links:

ENSG00000290199 (HGNC:):

ENSG00000290199 links:

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new If you want to explore the variant's impact on the transcript NM_001080843.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080843.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTT2B	NM_001080843.4	MANE Select	c.352-15C>G		intron	N/A	NP_001074312.1	P0CG30
	GSTT2B	NM_001363804.1		c.352-15C>G		intron	N/A	NP_001350733.1	Q6ICJ4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GSTT2B	ENST00000290765.9	TSL:1 MANE Select	c.352-15C>G	intron	N/A	ENSP00000290765.4	P0CG30
GSTT2B	ENST00000404172.3	TSL:1	c.352-15C>G	intron	N/A	ENSP00000385116.3	Q6ICJ4
GSTT2B	ENST00000895419.1		c.454-15C>G	intron	N/A	ENSP00000565478.1

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

98061

AN:

149876

Hom.:

27303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.668

Gnomad AMI

AF:

0.788

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.643

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.735

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.654

Gnomad OTH

AF:

0.647

GnomAD2 exomes

AF:

0.451

AC:

41501

AN:

92024

AF XY:

0.445

show subpopulations

Gnomad AFR exome

AF:

0.603

Gnomad AMR exome

AF:

0.412

Gnomad ASJ exome

AF:

0.403

Gnomad EAS exome

AF:

0.374

Gnomad FIN exome

AF:

0.549

Gnomad NFE exome

AF:

0.399

Gnomad OTH exome

AF:

0.488

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.653

AC:

937025

AN:

1434020

Hom.:

271116

Cov.:

AF XY:

0.655

AC XY:

467992

AN XY:

714234

show subpopulations

African (AFR)

AF:

0.671

AC:

22109

AN:

32948

American (AMR)

AF:

0.631

AC:

27774

AN:

44050

Ashkenazi Jewish (ASJ)

AF:

0.637

AC:

16425

AN:

25794

East Asian (EAS)

AF:

0.492

AC:

19433

AN:

39480

South Asian (SAS)

AF:

0.726

AC:

62090

AN:

85536

European-Finnish (FIN)

AF:

0.666

AC:

35464

AN:

53278

Middle Eastern (MID)

AF:

0.630

AC:

3559

AN:

5652

European-Non Finnish (NFE)

AF:

0.654

AC:

711783

AN:

1087952

Other (OTH)

AF:

0.647

AC:

38388

AN:

59330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

10359

20718

31078

41437

51796

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19588

39176

58764

78352

97940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.654

AC:

98145

AN:

149998

Hom.:

27330

Cov.:

AF XY:

0.656

AC XY:

48009

AN XY:

73240

show subpopulations

African (AFR)

AF:

0.668

AC:

27377

AN:

40988

American (AMR)

AF:

0.643

AC:

9664

AN:

15024

Ashkenazi Jewish (ASJ)

AF:

0.643

AC:

2207

AN:

3434

East Asian (EAS)

AF:

0.490

AC:

2485

AN:

5072

South Asian (SAS)

AF:

0.736

AC:

3489

AN:

4738

European-Finnish (FIN)

AF:

0.655

AC:

6815

AN:

10404

Middle Eastern (MID)

AF:

0.649

AC:

187

AN:

288

European-Non Finnish (NFE)

AF:

0.654

AC:

43882

AN:

67084

Other (OTH)

AF:

0.645

AC:

1341

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

1108

2216

3324

4432

5540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

846

1692

2538

3384

4230

<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:

0.575

Hom.:

1382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.0

(source)

DANN

Benign

0.81

PhyloP100

0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over