Variant 6-52984432-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001512.4(GSTA4):c.414+32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0581 in 1,583,256 control chromosomes in the GnomAD database, including 3,049 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 0.046 ( 228 hom., cov: 32)

Exomes 𝑓: 0.059 ( 2821 hom. )

Consequence

GSTA4
NM_001512.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.857

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
GSTA4	NM_001512.4 linkuse as main transcript	c.414+32C>T	intron_variant	ENST00000370963.9
GSTA4	XM_005249035.5 linkuse as main transcript	c.414+32C>T	intron_variant
GSTA4	XM_011514534.4 linkuse as main transcript	c.303+32C>T	intron_variant
GSTA4	XM_011514535.4 linkuse as main transcript	c.303+32C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTA4	ENST00000370963.9 linkuse as main transcript	c.414+32C>T		intron_variant		1	NM_001512.4	P1	O15217-1

Frequencies

GnomAD3 genomes

AF:

0.0464

AC:

7062

AN:

152168

Hom.:

228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0469

Gnomad ASJ

AF:

0.0727

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0363

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0674

Gnomad OTH

AF:

0.0463

GnomAD3 exomes

AF:

0.0482

AC:

11142

AN:

231044

Hom.:

330

AF XY:

0.0496

AC XY:

6217

AN XY:

125418

show subpopulations

Gnomad AFR exome

AF:

0.0102

Gnomad AMR exome

AF:

0.0276

Gnomad ASJ exome

AF:

0.0732

Gnomad EAS exome

AF:

0.000233

Gnomad SAS exome

AF:

0.0325

Gnomad FIN exome

AF:

0.0628

Gnomad NFE exome

AF:

0.0654

Gnomad OTH exome

AF:

0.0494

GnomAD4 exome

AF:

0.0593

AC:

84897

AN:

1430970

Hom.:

2821

Cov.:

AF XY:

0.0588

AC XY:

41866

AN XY:

712072

show subpopulations

Gnomad4 AFR exome

AF:

0.00850

Gnomad4 AMR exome

AF:

0.0290

Gnomad4 ASJ exome

AF:

0.0732

Gnomad4 EAS exome

AF:

0.000127

Gnomad4 SAS exome

AF:

0.0344

Gnomad4 FIN exome

AF:

0.0659

Gnomad4 NFE exome

AF:

0.0656

Gnomad4 OTH exome

AF:

0.0546

GnomAD4 genome

AF:

0.0464

AC:

7059

AN:

152286

Hom.:

228

Cov.:

AF XY:

0.0447

AC XY:

3332

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0117

Gnomad4 AMR

AF:

0.0468

Gnomad4 ASJ

AF:

0.0727

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0361

Gnomad4 FIN

AF:

0.0665

Gnomad4 NFE

AF:

0.0674

Gnomad4 OTH

AF:

0.0458

Alfa

AF:

0.0631

Hom.:

486

Bravo

AF:

0.0443

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.3

DANN

Benign

0.20

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over