6-52803872-T-C

Variant names:

• chr6-52803872-T-C
• rs3957356
• ENST00000867629.1:c.-277A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000867629.1(GSTA1):​c.-277A>G variant causes a 5 prime UTR 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 ENST00000867629.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 53 publications found

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]

ENSG00000301369 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000867629.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA1	NM_145740.5	MANE Select	c.-118A>G		upstream_gene	N/A	NP_665683.1	P08263
	GSTA1	NM_001319059.2		c.-264A>G		upstream_gene	N/A	NP_001305988.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA1	ENST00000867629.1		c.-277A>G		5_prime_UTR	Exon 1 of 8	ENSP00000537688.1
	ENSG00000301369	ENST00000778528.1		n.118+2669T>C		intron	N/A
	ENSG00000301369	ENST00000778529.1		n.63+1987T>C		intron	N/A

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

African (AFR) AF: 0.657 AC: 1664 AN: 2532

American (AMR) AF: 0.683 AC: 1111 AN: 1626

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1923 AN: 3696

East Asian (EAS) AF: 0.863 AC: 7422 AN: 8596

South Asian (SAS) AF: 0.647 AC: 313 AN: 484

European-Finnish (FIN) AF: 0.571 AC: 24 AN: 42

Middle Eastern (MID) AF: 0.511 AC: 180 AN: 352

European-Non Finnish (NFE) AF: 0.543 AC: 19100 AN: 35164

Other (OTH) AF: 0.574 AC: 2756 AN: 4802

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

African (AFR) AF: 0.685 AC: 28348 AN: 41410

American (AMR) AF: 0.698 AC: 10670 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3466

East Asian (EAS) AF: 0.873 AC: 4516 AN: 5172

South Asian (SAS) AF: 0.659 AC: 3163 AN: 4798

European-Finnish (FIN) AF: 0.563 AC: 5937 AN: 10544

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39011 AN: 67896

Other (OTH) AF: 0.633 AC: 1334 AN: 2106

Alfa AF: 0.645 Hom.: 11973

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.70
PhyloP100		-0.061
PromoterAI		0.43	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3957356; hg19: chr6-52668670;