rs2297235

chr10-104274733-A-G

Variant summary

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

The NM_183239.2(GSTO2):c.-183A>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 0.255 in 690,244 control chromosomes in the GnomAD database, including 24,170 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 0.22 (4330 hom., cov: 32)
  • Exomes 𝑓: 0.26 (19840 hom.)
• Consequence: GSTO2 NM_183239.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

Genes affected

GSTO2 (HGNC:23064): (glutathione S-transferase omega 2) The protein encoded by this gene is an omega class glutathione S-transferase (GST). GSTs are involved in the metabolism of xenobiotics and carcinogens. Four transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTO2	NM_183239.2	c.-183A>G		5_prime_UTR_variant	2/7	ENST00000338595.7
GSTO2	NM_001191013.2	c.-183A>G		5_prime_UTR_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTO2	ENST00000338595.7	c.-183A>G		5_prime_UTR_variant	2/7	1	NM_183239.2	P1
GSTO2	ENST00000450629.6	c.-183A>G		5_prime_UTR_variant	2/6	5

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33733 AN: 151992 Hom.: 4329 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.264 AC: 141953 AN: 538134 Hom.: 19840 Cov.: 7 AF XY: 0.261 AC XY: 74330 AN XY: 284482

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.192

Gnomad4 ASJ exome AF: 0.299

Gnomad4 EAS exome AF: 0.124

Gnomad4 SAS exome AF: 0.192

Gnomad4 FIN exome AF: 0.261

Gnomad4 NFE exome AF: 0.294

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.222 AC: 33745 AN: 152110 Hom.: 4330 Cov.: 32 AF XY: 0.219 AC XY: 16317 AN XY: 74366

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.246

Alfa AF: 0.273 Hom.: 3611

Bravo AF: 0.215

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.0
Dann	Benign	0.73

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: rs2297235; hg19: chr10-106034491;