rs11191972

Variant names:

• chr10-104247765-C-T
• rs11191972
• ENST00000470554.5:n.82-4401C>T

Variant summary

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

The ENST00000470554.5(GSTO1):​n.82-4401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,132 control chromosomes in the GnomAD database, including 5,105 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 0.26 (5105 hom., cov: 33)
• Consequence: GSTO1 ENST00000470554.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 12 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]

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 (NFE) allele frequency at 95% confidence interval = 0.288 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.82-4401C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38793 AN: 152014 Hom.: 5105 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.255 AC: 38815 AN: 152132 Hom.: 5105 Cov.: 33 AF XY: 0.252 AC XY: 18722 AN XY: 74364

African (AFR) AF: 0.229 AC: 9513 AN: 41494

American (AMR) AF: 0.218 AC: 3331 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.138 AC: 716 AN: 5182

South Asian (SAS) AF: 0.182 AC: 878 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2689 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19788 AN: 68004

Other (OTH) AF: 0.268 AC: 566 AN: 2114

Alfa AF: 0.264 Hom.: 811

Bravo AF: 0.253

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs11191972; hg19: chr10-106007523;