10-104265500-G-T

Variant names:

• chr10-104265500-G-T
• rs1147611
• NM_004832.3:c.466-584G>T

Variant summary

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

The NM_004832.3(GSTO1):​c.466-584G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,048 control chromosomes in the GnomAD database, including 18,685 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 0.46 (18685 hom., cov: 33)
• Consequence: GSTO1 NM_004832.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 21 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTO1	NM_004832.3	c.466-584G>T		intron_variant	Intron 4 of 5	ENST00000369713.10	NP_004823.1
GSTO1	NM_001191003.2	c.382-584G>T		intron_variant	Intron 4 of 5		NP_001177932.1
GSTO1	NM_001191002.2	c.367-584G>T		intron_variant	Intron 3 of 4		NP_001177931.1
LOC124902497	XR_007062284.1	n.365+3053C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO1	ENST00000369713.10	c.466-584G>T		intron_variant	Intron 4 of 5	1	NM_004832.3	ENSP00000358727.5

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69997 AN: 151928 Hom.: 18638 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.461 AC: 70096 AN: 152048 Hom.: 18685 Cov.: 33 AF XY: 0.453 AC XY: 33683 AN XY: 74314

African (AFR) AF: 0.744 AC: 30832 AN: 41452

American (AMR) AF: 0.345 AC: 5270 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1600 AN: 3466

East Asian (EAS) AF: 0.246 AC: 1274 AN: 5178

South Asian (SAS) AF: 0.350 AC: 1688 AN: 4826

European-Finnish (FIN) AF: 0.321 AC: 3400 AN: 10576

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.364 AC: 24751 AN: 67960

Other (OTH) AF: 0.452 AC: 953 AN: 2110

Alfa AF: 0.424 Hom.: 21830

Bravo AF: 0.476

Asia WGS AF: 0.346 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.1
DANN	Benign	0.77
PhyloP100		-0.22
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: rs1147611; hg19: chr10-106025258;