rs156699

Variant names:

• chr10-104293883-A-G
• rs156699
• NM_183239.2:c.469-3695A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GSTO2	NM_183239.2	c.469-3695A>G		intron_variant	Intron 5 of 6	ENST00000338595.7	NP_899062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO2	ENST00000338595.7	c.469-3695A>G		intron_variant	Intron 5 of 6	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

African (AFR) AF: 0.708 AC: 29325 AN: 41400

American (AMR) AF: 0.308 AC: 4699 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1213 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5170

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4818

European-Finnish (FIN) AF: 0.299 AC: 3157 AN: 10544

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21505 AN: 67938

Other (OTH) AF: 0.395 AC: 830 AN: 2100

Alfa AF: 0.351 Hom.: 33005

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
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs156699; hg19: chr10-106053641;