chr10-104293883-A-G

Position:

• chr10-104293883-A-G

Variant summary

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

The NM_183239.2(GSTO2):​c.469-3695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,920 control chromosomes in the GnomAD database, including 15,794 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 (15794 hom., cov: 31)
• Consequence: GSTO2 NM_183239.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSTO2	NM_183239.2	c.469-3695A>G		intron_variant		ENST00000338595.7	NP_899062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTO2	ENST00000338595.7	c.469-3695A>G		intron_variant		1	NM_183239.2	ENSP00000345023.1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63060 AN: 151800 Hom.: 15752 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.416 AC: 63149 AN: 151920 Hom.: 15794 Cov.: 31 AF XY: 0.409 AC XY: 30392 AN XY: 74258

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.395

Alfa AF: 0.329 Hom.: 17555

Bravo AF: 0.432

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.42

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: rs156699; hg19: chr10-106053641;