chr10-104299143-G-T

Position:

• chr10-104299143-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

GSTO2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSTO2	NM_183239.2	c.591G>T	p.Thr197Thr	synonymous_variant	7/7	ENST00000338595.7	NP_899062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTO2	ENST00000338595.7	c.591G>T	p.Thr197Thr	synonymous_variant	7/7	1	NM_183239.2	ENSP00000345023.1

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

GnomAD3 exomes AF: 0.0404 AC: 10120 AN: 250722 Hom.: 365 AF XY: 0.0365 AC XY: 4954 AN XY: 135584

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 SAS exome AF: 0.0249

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

Gnomad4 AFR exome AF: 0.133

Gnomad4 AMR exome AF: 0.0399

Gnomad4 ASJ exome AF: 0.0681

Gnomad4 EAS exome AF: 0.139

Gnomad4 SAS exome AF: 0.0261

Gnomad4 FIN exome AF: 0.0467

Gnomad4 NFE exome AF: 0.0148

Gnomad4 OTH exome AF: 0.0423

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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0330 Hom.: 168

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	4.2
DANN	Benign	0.96

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758572; hg19: chr10-106058901; COSMIC: COSV58538321;