chr6-52801475-T-C

Variant names:

• chr6-52801475-T-C
• rs6917325
• NM_145740.5:c.-30-2178A>G

Variant summary

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

The NM_145740.5(GSTA1):​c.-30-2178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,112 control chromosomes in the GnomAD database, including 31,324 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 0.64 (31324 hom., cov: 33)
• Consequence: GSTA1 NM_145740.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 19 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=-0.88).
• 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: NM_145740.5. 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.-30-2178A>G		intron	N/A	NP_665683.1	P08263
	GSTA1	NM_001319059.2		c.-176-2178A>G		intron	N/A	NP_001305988.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA1	ENST00000334575.6	TSL:1 MANE Select	c.-30-2178A>G		intron	N/A	ENSP00000335620.5	P08263
	GSTA1	ENST00000867635.1		c.-183A>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 7	ENSP00000537694.1
	GSTA1	ENST00000867635.1		c.-183A>G		5_prime_UTR	Exon 1 of 7	ENSP00000537694.1

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96561 AN: 151994 Hom.: 31303 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.629

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.635 AC: 96630 AN: 152112 Hom.: 31324 Cov.: 33 AF XY: 0.638 AC XY: 47466 AN XY: 74354

African (AFR) AF: 0.701 AC: 29099 AN: 41502

American (AMR) AF: 0.701 AC: 10717 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4512 AN: 5168

South Asian (SAS) AF: 0.660 AC: 3185 AN: 4826

European-Finnish (FIN) AF: 0.563 AC: 5938 AN: 10550

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

European-Non Finnish (NFE) AF: 0.575 AC: 39084 AN: 67988

Other (OTH) AF: 0.632 AC: 1337 AN: 2114

Alfa AF: 0.607 Hom.: 19806

Bravo AF: 0.649

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.51
PhyloP100		1.5
Mutation Taster		=100/0	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: rs6917325; hg19: chr6-52666273;