10-104253687-G-A

Variant names:

• chr10-104253687-G-A
• rs2164624
• ENST00000470554.5:n.106-777G>A

Variant summary

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

The ENST00000470554.5(GSTO1):​n.106-777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,090 control chromosomes in the GnomAD database, including 5,550 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 0.25 (5550 hom., cov: 32)
• Consequence: GSTO1 ENST00000470554.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 14 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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470554.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO1	ENST00000470554.5	TSL:2	n.106-777G>A		intron	N/A
	ENSG00000302058	ENST00000783699.1		n.439-5095C>T		intron	N/A
	ENSG00000302058	ENST00000783700.1		n.303-5095C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38386 AN: 151972 Hom.: 5547 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.253 AC: 38404 AN: 152090 Hom.: 5550 Cov.: 32 AF XY: 0.250 AC XY: 18562 AN XY: 74326

African (AFR) AF: 0.125 AC: 5204 AN: 41500

American (AMR) AF: 0.243 AC: 3720 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1398 AN: 3464

East Asian (EAS) AF: 0.109 AC: 565 AN: 5180

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4816

European-Finnish (FIN) AF: 0.280 AC: 2952 AN: 10560

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22560 AN: 67976

Other (OTH) AF: 0.288 AC: 608 AN: 2108

Alfa AF: 0.255 Hom.: 1715

Bravo AF: 0.245

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.0
DANN	Benign	0.81
PhyloP100		0.019

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2164624; hg19: chr10-106013445;