rs11191972

chr10-104247765-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000470554.5(GSTO1):n.82-4401C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTO1	ENST00000470554.5	n.82-4401C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.268

Alfa AF: 0.265 Hom.: 787

Bravo AF: 0.253

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11191972; hg19: chr10-106007523;