Genetic Variant GSTA4:c.*429G>A (chr6-52978041-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001512.4(GSTA4):c.*429G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 157,360 control chromosomes in the GnomAD database, including 2,743 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 0.17 ( 2716 hom., cov: 32)

Exomes 𝑓: 0.11 ( 27 hom. )

Consequence

GSTA4
NM_001512.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

Publications

16 publications found

Variant links:

Genes affected

GSTA4 (HGNC:4629): (glutathione S-transferase alpha 4) Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. These enzymes are involved in cellular defense against toxic, carcinogenic, and pharmacologically active electrophilic compounds. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-tranferase belonging to the alpha class. The alpha class genes, which are located in a cluster on chromosome 6, are highly related and encode enzymes with glutathione peroxidase activity that function in the detoxification of lipid peroxidation products. Reactive electrophiles produced by oxidative metabolism have been linked to a number of degenerative diseases including Parkinson's disease, Alzheimer's disease, cataract formation, and atherosclerosis. [provided by RefSeq, Jul 2008]

GSTA4 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GSTA4	NM_001512.4 link	c.*429G>A	3_prime_UTR_variant	Exon 7 of 7	ENST00000370963.9	NP_001503.1	O15217-1A0A024RD58
GSTA4	XM_005249035.5 link	c.*429G>A	3_prime_UTR_variant	Exon 7 of 7		XP_005249092.1	O15217-1A0A024RD58
GSTA4	XM_011514534.4 link	c.*429G>A	3_prime_UTR_variant	Exon 6 of 6		XP_011512836.1
GSTA4	XM_011514535.4 link	c.*429G>A	3_prime_UTR_variant	Exon 6 of 6		XP_011512837.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GSTA4	ENST00000370963.9 link	c.*429G>A	3_prime_UTR_variant	Exon 7 of 7	1	NM_001512.4	ENSP00000360002.4	O15217-1
GSTA4	ENST00000477599.5 link	n.1039G>A	non_coding_transcript_exon_variant	Exon 6 of 6	3
GSTA4	ENST00000486559.5 link	n.1605G>A	non_coding_transcript_exon_variant	Exon 5 of 5	2
GSTA4	ENST00000370960.5 link	c.*429G>A	downstream_gene_variant		3		ENSP00000359999.1	O15217-2

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25900

AN:

151938

Hom.:

2696

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.161

GnomAD4 exome

AF:

0.109

AC:

579

AN:

5304

Hom.:

Cov.:

AF XY:

0.108

AC XY:

284

AN XY:

2626

show subpopulations

African (AFR)

AF:

0.242

AC:

AN:

American (AMR)

AF:

0.234

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

AN:

East Asian (EAS)

AF:

0.0357

AC:

AN:

South Asian (SAS)

AF:

0.122

AC:

AN:

278

European-Finnish (FIN)

AF:

0.0812

AC:

AN:

234

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.104

AC:

427

AN:

4104

Other (OTH)

AF:

0.130

AC:

AN:

378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

114

143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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

AF:

0.171

AC:

25967

AN:

152056

Hom.:

2716

Cov.:

AF XY:

0.172

AC XY:

12755

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.260

AC:

10773

AN:

41436

American (AMR)

AF:

0.268

AC:

4098

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.155

AC:

537

AN:

3470

East Asian (EAS)

AF:

0.132

AC:

682

AN:

5176

South Asian (SAS)

AF:

0.184

AC:

886

AN:

4818

European-Finnish (FIN)

AF:

0.107

AC:

1132

AN:

10572

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7317

AN:

67986

Other (OTH)

AF:

0.162

AC:

342

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1054

2109

3163

4218

5272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.126

Hom.:

4134

Bravo

AF:

0.184

Asia WGS

AF:

0.191

AC:

665

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.7

(source)

DANN

Benign

0.40

PhyloP100

0.033

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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