10-104296205-C-A

Position:

• chr10-104296205-C-A

Variant summary

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

The NM_183239.2(GSTO2):​c.469-1373C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,912 control chromosomes in the GnomAD database, including 15,757 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 0.42 (15757 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: GSTO2 NM_183239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTO2	NM_183239.2	c.469-1373C>A		intron_variant		ENST00000338595.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTO2	ENST00000338595.7	c.469-1373C>A		intron_variant		1	NM_183239.2	P1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63002 AN: 151790 Hom.: 15715 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.397

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.415 AC: 63090 AN: 151910 Hom.: 15757 Cov.: 31 AF XY: 0.409 AC XY: 30357 AN XY: 74216

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.394

Alfa AF: 0.321 Hom.: 10729

Bravo AF: 0.432

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0020
DANN	Benign	0.40

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: rs157080; hg19: chr10-106055963;