rs3734431

chr6-52978631-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001512.4(GSTA4):c.547-39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 1,538,188 control chromosomes in the GnomAD database, including 4,625 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 0.077 (458 hom., cov: 32)
  • Exomes 𝑓: 0.076 (4167 hom.)
• Consequence: GSTA4 NM_001512.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTA4	NM_001512.4	c.547-39T>C		intron_variant		ENST00000370963.9
GSTA4	XM_005249035.5	c.547-39T>C		intron_variant
GSTA4	XM_011514534.4	c.436-39T>C		intron_variant
GSTA4	XM_011514535.4	c.436-39T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTA4	ENST00000370963.9	c.547-39T>C		intron_variant		1	NM_001512.4	P1

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11650 AN: 152124 Hom.: 457 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.0844

GnomAD3 exomes AF: 0.0778 AC: 17738 AN: 227940 Hom.: 758 AF XY: 0.0790 AC XY: 9751 AN XY: 123500

Gnomad AFR exome AF: 0.0656

Gnomad AMR exome AF: 0.0715

Gnomad ASJ exome AF: 0.0995

Gnomad EAS exome AF: 0.0773

Gnomad SAS exome AF: 0.0836

Gnomad FIN exome AF: 0.0539

Gnomad NFE exome AF: 0.0821

Gnomad OTH exome AF: 0.0877

GnomAD4 exome AF: 0.0761 AC: 105486 AN: 1385946 Hom.: 4167 Cov.: 22 AF XY: 0.0766 AC XY: 53016 AN XY: 692150

Gnomad4 AFR exome AF: 0.0654

Gnomad4 AMR exome AF: 0.0710

Gnomad4 ASJ exome AF: 0.0941

Gnomad4 EAS exome AF: 0.0680

Gnomad4 SAS exome AF: 0.0841

Gnomad4 FIN exome AF: 0.0540

Gnomad4 NFE exome AF: 0.0766

Gnomad4 OTH exome AF: 0.0795

GnomAD4 genome AF: 0.0766 AC: 11660 AN: 152242 Hom.: 458 Cov.: 32 AF XY: 0.0764 AC XY: 5691 AN XY: 74446

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.0644

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0840

Gnomad4 OTH AF: 0.0830

Alfa AF: 0.0847 Hom.: 833

Bravo AF: 0.0785

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.33
Dann	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734431; hg19: chr6-52843429;