10-104299143-G-T

Variant names:

• chr10-104299143-G-T
• rs3758572
• NM_183239.2:c.591G>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_183239.2(GSTO2):​c.591G>T​(p.Thr197Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0286 in 1,613,820 control chromosomes in the GnomAD database, including 1,562 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 0.057 (415 hom., cov: 33)
  • Exomes 𝑓: 0.026 (1147 hom.)
• Consequence: GSTO2 NM_183239.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 9 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.004).
• BP7: Synonymous conserved (PhyloP=0.01 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	NM_183239.2	MANE Select	c.591G>T	p.Thr197Thr	synonymous	Exon 7 of 7	NP_899062.1
	GSTO2	NM_001191014.2		c.507G>T	p.Thr169Thr	synonymous	Exon 5 of 5	NP_001177943.1
	GSTO2	NM_001191013.2		c.489G>T	p.Thr163Thr	synonymous	Exon 6 of 6	NP_001177942.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	ENST00000338595.7	TSL:1 MANE Select	c.591G>T	p.Thr197Thr	synonymous	Exon 7 of 7	ENSP00000345023.1
	GSTO2	ENST00000369707.2	TSL:1	c.507G>T	p.Thr169Thr	synonymous	Exon 5 of 5	ENSP00000358721.1
	GSTO2	ENST00000450629.6	TSL:5	c.489G>T	p.Thr163Thr	synonymous	Exon 6 of 6	ENSP00000390986.2

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8636 AN: 152118 Hom.: 412 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0531

GnomAD2 exomes AF: 0.0404 AC: 10120 AN: 250722 AF XY: 0.0365

Gnomad AFR exome AF: 0.132

Gnomad AMR exome AF: 0.0401

Gnomad ASJ exome AF: 0.0638

Gnomad EAS exome AF: 0.111

Gnomad FIN exome AF: 0.0457

Gnomad NFE exome AF: 0.0169

Gnomad OTH exome AF: 0.0400

GnomAD4 exome AF: 0.0256 AC: 37459 AN: 1461584 Hom.: 1147 Cov.: 31 AF XY: 0.0250 AC XY: 18193 AN XY: 727070

African (AFR) AF: 0.133 AC: 4442 AN: 33472

American (AMR) AF: 0.0399 AC: 1782 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.0681 AC: 1779 AN: 26128

East Asian (EAS) AF: 0.139 AC: 5509 AN: 39688

South Asian (SAS) AF: 0.0261 AC: 2251 AN: 86240

European-Finnish (FIN) AF: 0.0467 AC: 2494 AN: 53372

Middle Eastern (MID) AF: 0.0410 AC: 234 AN: 5702

European-Non Finnish (NFE) AF: 0.0148 AC: 16416 AN: 1111892

Other (OTH) AF: 0.0423 AC: 2552 AN: 60380

GnomAD4 genome AF: 0.0569 AC: 8659 AN: 152236 Hom.: 415 Cov.: 33 AF XY: 0.0581 AC XY: 4324 AN XY: 74444

African (AFR) AF: 0.129 AC: 5353 AN: 41528

American (AMR) AF: 0.0395 AC: 605 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.117 AC: 605 AN: 5170

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4832

European-Finnish (FIN) AF: 0.0443 AC: 470 AN: 10598

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0167 AC: 1137 AN: 68014

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0349 Hom.: 502

Bravo AF: 0.0614

Asia WGS AF: 0.111 AC: 387 AN: 3478

EpiCase AF: 0.0176

EpiControl AF: 0.0154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	4.2
DANN	Benign	0.96
PhyloP100		0.010
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3758572; hg19: chr10-106058901; COSMIC: COSV58538321;