rs157080

Variant names:

• chr10-104296205-C-A
• rs157080
• NM_183239.2:c.469-1373C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-104296205-C-A
• chr10-104296205-C-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.469-1373C>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
• Publications: 14 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=-0.95).
• 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 rank	MANE	Protein	UniProt
GSTO2	NM_183239.2	c.469-1373C>A		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.469-1373C>A		intron_variant	Intron 5 of 6	1	NM_183239.2	ENSP00000345023.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.708 AC: 29298 AN: 41396

American (AMR) AF: 0.308 AC: 4705 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1032 AN: 5168

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4816

European-Finnish (FIN) AF: 0.302 AC: 3176 AN: 10516

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

European-Non Finnish (NFE) AF: 0.316 AC: 21488 AN: 67948

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.360 Hom.: 21174

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
PhyloP100		-1.8
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: rs157080; hg19: chr10-106055963;