rs10491045

chr10-104274145-T-C

Variant summary

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

The NM_183239.2(GSTO2):c.-231-540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.035 in 152,250 control chromosomes in the GnomAD database, including 121 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 0.035 (121 hom., cov: 32)
• Consequence: GSTO2 NM_183239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTO2	NM_183239.2	c.-231-540T>C		intron_variant		ENST00000338595.7
GSTO2	NM_001191013.2	c.-231-540T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTO2	ENST00000338595.7	c.-231-540T>C		intron_variant		1	NM_183239.2	P1
GSTO2	ENST00000450629.6	c.-231-540T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5334 AN: 152132 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.00896

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0311

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0350 AC: 5333 AN: 152250 Hom.: 121 Cov.: 32 AF XY: 0.0343 AC XY: 2552 AN XY: 74436

Gnomad4 AFR AF: 0.00893

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00373

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0463 Hom.: 238

Bravo AF: 0.0320

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.5
Dann	Benign	0.59

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: rs10491045; hg19: chr10-106033903;