chr10-104260640-A-C

Variant names:

• chr10-104260640-A-C
• rs2282326
• NM_004832.3:c.366+842A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004832.3(GSTO1):​c.366+842A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,110 control chromosomes in the GnomAD database, including 17,362 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 0.45 (17362 hom., cov: 33)
• Consequence: GSTO1 NM_004832.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 20 publications found

Genes affected

GSTO1 (HGNC:13312): (glutathione S-transferase omega 1) The protein encoded by this gene is an omega class glutathione S-transferase (GST) with glutathione-dependent thiol transferase and dehydroascorbate reductase activities. GSTs are involved in the metabolism of xenobiotics and carcinogens. The encoded protein acts as a homodimer and is found in the cytoplasm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

ENSG00000302058 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTO1	NM_004832.3	c.366+842A>C		intron_variant	Intron 3 of 5	ENST00000369713.10	NP_004823.1
GSTO1	NM_001191003.2	c.282+842A>C		intron_variant	Intron 3 of 5		NP_001177932.1
GSTO1	NM_001191002.2	c.366+842A>C		intron_variant	Intron 3 of 4		NP_001177931.1
LOC124902497	XR_007062284.1	n.365+7913T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO1	ENST00000369713.10	c.366+842A>C		intron_variant	Intron 3 of 5	1	NM_004832.3	ENSP00000358727.5

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68180 AN: 151992 Hom.: 17318 Cov.: 33

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.449 AC: 68274 AN: 152110 Hom.: 17362 Cov.: 33 AF XY: 0.441 AC XY: 32808 AN XY: 74368

African (AFR) AF: 0.699 AC: 29010 AN: 41476

American (AMR) AF: 0.341 AC: 5217 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1640 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1289 AN: 5180

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4814

European-Finnish (FIN) AF: 0.321 AC: 3400 AN: 10586

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24767 AN: 67976

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.444 Hom.: 3059

Bravo AF: 0.463

Asia WGS AF: 0.346 AC: 1204 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.80
DANN	Benign	0.77
PhyloP100		-2.4
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: rs2282326; hg19: chr10-106020398;