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. The variant received -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
• Publications: 22 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183239.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	NM_183239.2	MANE Select	c.366+20T>C		intron	N/A	NP_899062.1
	GSTO2	NM_001191014.2		c.282+20T>C		intron	N/A	NP_001177943.1
	GSTO2	NM_001191013.2		c.366+20T>C		intron	N/A	NP_001177942.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	ENST00000338595.7	TSL:1 MANE Select	c.366+20T>C		intron	N/A	ENSP00000345023.1
	GSTO2	ENST00000369707.2	TSL:1	c.282+20T>C		intron	N/A	ENSP00000358721.1
	GSTO2	ENST00000450629.6	TSL:5	c.366+20T>C		intron	N/A	ENSP00000390986.2

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

GnomAD2 exomes AF: 0.449 AC: 109286 AN: 243144 AF XY: 0.452

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 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

African (AFR) AF: 0.775 AC: 25501 AN: 32908

American (AMR) AF: 0.304 AC: 13388 AN: 44070

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 13436 AN: 25896

East Asian (EAS) AF: 0.386 AC: 15234 AN: 39464

South Asian (SAS) AF: 0.486 AC: 41379 AN: 85128

European-Finnish (FIN) AF: 0.397 AC: 21110 AN: 53130

Middle Eastern (MID) AF: 0.546 AC: 2587 AN: 4736

European-Non Finnish (NFE) AF: 0.446 AC: 484026 AN: 1084938

Other (OTH) AF: 0.470 AC: 27787 AN: 59160

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

African (AFR) AF: 0.764 AC: 31726 AN: 41514

American (AMR) AF: 0.411 AC: 6286 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2121 AN: 5174

South Asian (SAS) AF: 0.480 AC: 2315 AN: 4822

European-Finnish (FIN) AF: 0.381 AC: 4026 AN: 10564

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30417 AN: 67944

Other (OTH) AF: 0.525 AC: 1109 AN: 2114

Alfa AF: 0.497 Hom.: 33305

Bravo AF: 0.540

Asia WGS AF: 0.473 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.47
PhyloP100		-1.5
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: rs157077; hg19: chr10-106037894; COSMIC: COSV58538303;