6-52803872-T-C

Position:

• chr6-52803872-T-C

Variant summary

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

The 6-52803872-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 209,168 control chromosomes in the GnomAD database, including 41,541 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 0.63 (30761 hom., cov: 32)
  • Exomes 𝑓: 0.60 (10780 hom.)
• Consequence: GSTA1 ENST00000476213.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

GSTA1 (HGNC:4626): (glutathione S-transferase alpha 1) This gene encodes a member of a family of enzymes that function to add glutathione to target electrophilic compounds, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. This action is an important step in detoxification of these compounds. This subfamily of enzymes has a particular role in protecting cells from reactive oxygen species and the products of peroxidation. Polymorphisms in this gene influence the ability of individuals to metabolize different drugs. This gene is located in a cluster of similar genes and pseudogenes on chromosome 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTA1	ENST00000476213.1			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95662 AN: 151756 Hom.: 30742 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.630

GnomAD4 exome AF: 0.602 AC: 34493 AN: 57294 Hom.: 10780 Cov.: 0 AF XY: 0.598 AC XY: 15860 AN XY: 26532

Gnomad4 AFR exome AF: 0.657

Gnomad4 AMR exome AF: 0.683

Gnomad4 ASJ exome AF: 0.520

Gnomad4 EAS exome AF: 0.863

Gnomad4 SAS exome AF: 0.647

Gnomad4 FIN exome AF: 0.571

Gnomad4 NFE exome AF: 0.543

Gnomad4 OTH exome AF: 0.574

GnomAD4 genome AF: 0.630 AC: 95728 AN: 151874 Hom.: 30761 Cov.: 32 AF XY: 0.633 AC XY: 47014 AN XY: 74224

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.633

Alfa AF: 0.621 Hom.: 3780

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.70

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: rs3957356; hg19: chr6-52668670;