rs17614751

Variant names:

• chr6-52978051-G-A
• rs17614751
• NM_001512.4:c.*419C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-52978051-G-A
• chr6-52978051-G-C
• chr6-52978051-G-T

Variant summary

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

The NM_001512.4(GSTA4):​c.*419C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 157,476 control chromosomes in the GnomAD database, including 245 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 (229 hom., cov: 32)
  • Exomes 𝑓: 0.068 (16 hom.)
• Consequence: GSTA4 NM_001512.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001512.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA4	NM_001512.4	MANE Select	c.*419C>T		3_prime_UTR	Exon 7 of 7	NP_001503.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA4	ENST00000370963.9	TSL:1 MANE Select	c.*419C>T		3_prime_UTR	Exon 7 of 7	ENSP00000360002.4
	GSTA4	ENST00000477599.5	TSL:3	n.1029C>T		non_coding_transcript_exon	Exon 6 of 6
	GSTA4	ENST00000486559.5	TSL:2	n.1595C>T		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7063 AN: 151898 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0374

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.0460

GnomAD4 exome AF: 0.0678 AC: 370 AN: 5460 Hom.: 16 Cov.: 0 AF XY: 0.0694 AC XY: 187 AN XY: 2696

African (AFR) AF: 0.0263 AC: 2 AN: 76

American (AMR) AF: 0.0789 AC: 6 AN: 76

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 10 AN: 112

East Asian (EAS) AF: 0.00 AC: 0 AN: 66

South Asian (SAS) AF: 0.0476 AC: 14 AN: 294

European-Finnish (FIN) AF: 0.0744 AC: 18 AN: 242

Middle Eastern (MID) AF: 0.0313 AC: 1 AN: 32

European-Non Finnish (NFE) AF: 0.0709 AC: 297 AN: 4188

Other (OTH) AF: 0.0588 AC: 22 AN: 374

GnomAD4 genome AF: 0.0464 AC: 7060 AN: 152016 Hom.: 229 Cov.: 32 AF XY: 0.0449 AC XY: 3335 AN XY: 74308

African (AFR) AF: 0.0117 AC: 485 AN: 41430

American (AMR) AF: 0.0469 AC: 717 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0373 AC: 179 AN: 4804

European-Finnish (FIN) AF: 0.0666 AC: 704 AN: 10566

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0674 AC: 4581 AN: 67968

Other (OTH) AF: 0.0455 AC: 96 AN: 2108

Alfa AF: 0.0585 Hom.: 837

Bravo AF: 0.0443

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17614751; hg19: chr6-52842849;