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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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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTT2B	NM_001080843.4 link	c.352-15C>G		intron_variant	Intron 3 of 4	ENST00000290765.9	NP_001074312.1	P0CG30G9J6Q5
GSTT2B	NM_001363804.1 link	c.352-15C>G		intron_variant	Intron 3 of 4		NP_001350733.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTT2B	ENST00000290765.9 link	c.352-15C>G		intron_variant	Intron 3 of 4	1	NM_001080843.4	ENSP00000290765.4		P0CG30

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over