NM_183239.2:c.366+20T>C

Variant names:

• chr10-104278136-T-C
• rs157077
• NM_183239.2:c.366+20T>C

Variant summary

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

The NM_183239.2(GSTO2):​c.366+20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,581,530 control chromosomes in the GnomAD database, including 171,336 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 0.53 (23017 hom., cov: 33)
  • Exomes 𝑓: 0.45 (148319 hom.)
• Consequence: GSTO2 NM_183239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTO2	NM_183239.2	c.366+20T>C		intron_variant	Intron 4 of 6	ENST00000338595.7	NP_899062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO2	ENST00000338595.7	c.366+20T>C		intron_variant	Intron 4 of 6	1	NM_183239.2	ENSP00000345023.1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80258 AN: 151980 Hom.: 22971 Cov.: 33

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.527

GnomAD3 exomes AF: 0.449 AC: 109286 AN: 243144 Hom.: 25906 AF XY: 0.452 AC XY: 59416 AN XY: 131346

Gnomad AFR exome AF: 0.769

Gnomad AMR exome AF: 0.293

Gnomad ASJ exome AF: 0.512

Gnomad EAS exome AF: 0.402

Gnomad SAS exome AF: 0.485

Gnomad FIN exome AF: 0.398

Gnomad NFE exome AF: 0.453

Gnomad OTH exome AF: 0.465

GnomAD4 exome AF: 0.451 AC: 644448 AN: 1429430 Hom.: 148319 Cov.: 24 AF XY: 0.452 AC XY: 321961 AN XY: 712390

Gnomad4 AFR exome AF: 0.775

Gnomad4 AMR exome AF: 0.304

Gnomad4 ASJ exome AF: 0.519

Gnomad4 EAS exome AF: 0.386

Gnomad4 SAS exome AF: 0.486

Gnomad4 FIN exome AF: 0.397

Gnomad4 NFE exome AF: 0.446

Gnomad4 OTH exome AF: 0.470

GnomAD4 genome AF: 0.528 AC: 80354 AN: 152100 Hom.: 23017 Cov.: 33 AF XY: 0.522 AC XY: 38827 AN XY: 74336

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.525

Alfa AF: 0.470 Hom.: 18042

Bravo AF: 0.540

Asia WGS AF: 0.473 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.47

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: rs157077; hg19: chr10-106037894; COSMIC: COSV58538303;