rs11509435

Positions:

• chr10-104255006-CCGG-C
• chr10-104255006-CCGG-CCGGCGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004832.3(GSTO1):​c.34+49_34+51del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,574,656 control chromosomes in the GnomAD database, including 61,750 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.23 (4467 hom., cov: 26)
  • Exomes 𝑓: 0.28 (57283 hom.)
• Consequence: GSTO1 NM_004832.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

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]

LOC124902497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTO1	NM_004832.3	c.34+49_34+51del		intron_variant		ENST00000369713.10
LOC124902497	XR_007062284.1	n.366-6417_366-6415del		intron_variant, non_coding_transcript_variant
GSTO1	NM_001191002.2	c.34+49_34+51del		intron_variant
GSTO1	NM_001191003.2	c.-50-152_-50-150del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTO1	ENST00000369713.10	c.34+49_34+51del		intron_variant		1	NM_004832.3	P1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34415 AN: 151836 Hom.: 4466 Cov.: 26

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.261

GnomAD3 exomes AF: 0.241 AC: 49221 AN: 204394 Hom.: 6441 AF XY: 0.246 AC XY: 27386 AN XY: 111416

Gnomad AFR exome AF: 0.0949

Gnomad AMR exome AF: 0.178

Gnomad ASJ exome AF: 0.323

Gnomad EAS exome AF: 0.139

Gnomad SAS exome AF: 0.192

Gnomad FIN exome AF: 0.268

Gnomad NFE exome AF: 0.299

Gnomad OTH exome AF: 0.280

GnomAD4 exome AF: 0.277 AC: 394252 AN: 1422702 Hom.: 57283 AF XY: 0.276 AC XY: 195177 AN XY: 706724

Gnomad4 AFR exome AF: 0.0942

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.319

Gnomad4 EAS exome AF: 0.128

Gnomad4 SAS exome AF: 0.194

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.265

GnomAD4 genome AF: 0.227 AC: 34425 AN: 151954 Hom.: 4467 Cov.: 26 AF XY: 0.223 AC XY: 16593 AN XY: 74256

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.259

Alfa AF: 0.274 Hom.: 1127

Bravo AF: 0.220

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11509435; hg19: chr10-106014764;