rs2297235

Variant names:

• chr10-104274733-A-G
• rs2297235
• NM_183239.2:c.-183A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 42 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183239.2. 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
	GSTO2	NM_183239.2	MANE Select	c.-183A>G		5_prime_UTR	Exon 2 of 7	NP_899062.1	Q9H4Y5-1
	GSTO2	NM_001191013.2		c.-183A>G		5_prime_UTR	Exon 2 of 6	NP_001177942.1	Q9H4Y5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	ENST00000338595.7	TSL:1 MANE Select	c.-183A>G		5_prime_UTR	Exon 2 of 7	ENSP00000345023.1	Q9H4Y5-1
	GSTO2	ENST00000912037.1		c.-183A>G		5_prime_UTR	Exon 2 of 7	ENSP00000582096.1
	GSTO2	ENST00000450629.6	TSL:5	c.-183A>G		5_prime_UTR	Exon 2 of 6	ENSP00000390986.2	Q9H4Y5-2

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

African (AFR) AF: 0.100 AC: 1218 AN: 12154

American (AMR) AF: 0.192 AC: 3350 AN: 17464

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 4592 AN: 15350

East Asian (EAS) AF: 0.124 AC: 3531 AN: 28482

South Asian (SAS) AF: 0.192 AC: 9681 AN: 50414

European-Finnish (FIN) AF: 0.261 AC: 9984 AN: 38296

Middle Eastern (MID) AF: 0.290 AC: 656 AN: 2262

European-Non Finnish (NFE) AF: 0.294 AC: 101581 AN: 344994

Other (OTH) AF: 0.256 AC: 7360 AN: 28718

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

African (AFR) AF: 0.100 AC: 4152 AN: 41490

American (AMR) AF: 0.217 AC: 3325 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3466

East Asian (EAS) AF: 0.139 AC: 716 AN: 5168

South Asian (SAS) AF: 0.193 AC: 929 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2689 AN: 10576

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20047 AN: 67974

Other (OTH) AF: 0.246 AC: 521 AN: 2114

Alfa AF: 0.253 Hom.: 5362

Bravo AF: 0.215

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		-0.33
PromoterAI		-0.039	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: rs2297235; hg19: chr10-106034491;