rs11509435

Variant names:

• chr10-104255006-CCGG-C
• rs11509435
• NM_004832.3:c.34+49_34+51delGGC

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_004832.3(GSTO1):​c.34+49_34+51delGGC 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
• Publications: 2 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 -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004832.3. 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
	GSTO1	NM_004832.3	MANE Select	c.34+49_34+51delGGC		intron	N/A	NP_004823.1	P78417-1
	GSTO1	NM_001191003.2		c.-50-152_-50-150delGGC		intron	N/A	NP_001177932.1	P78417-3
	GSTO1	NM_001191002.2		c.34+49_34+51delGGC		intron	N/A	NP_001177931.1	P78417-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO1	ENST00000369713.10	TSL:1 MANE Select	c.34+49_34+51delGGC		intron	N/A	ENSP00000358727.5	P78417-1
	GSTO1	ENST00000445155.5	TSL:2	c.-202_-200delGGC		5_prime_UTR	Exon 1 of 5	ENSP00000406708.1	Q5TA02
	GSTO1	ENST00000539281.5	TSL:5	c.-50-152_-50-150delGGC		intron	N/A	ENSP00000441488.1	P78417-3

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

GnomAD2 exomes AF: 0.241 AC: 49221 AN: 204394 AF XY: 0.246

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 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

African (AFR) AF: 0.0942 AC: 3099 AN: 32910

American (AMR) AF: 0.181 AC: 7451 AN: 41106

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 7954 AN: 24954

East Asian (EAS) AF: 0.128 AC: 4993 AN: 38960

South Asian (SAS) AF: 0.194 AC: 16154 AN: 83086

European-Finnish (FIN) AF: 0.268 AC: 13645 AN: 51000

Middle Eastern (MID) AF: 0.322 AC: 1774 AN: 5512

European-Non Finnish (NFE) AF: 0.298 AC: 323613 AN: 1086322

Other (OTH) AF: 0.265 AC: 15569 AN: 58852

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

African (AFR) AF: 0.0995 AC: 4130 AN: 41508

American (AMR) AF: 0.221 AC: 3372 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3464

East Asian (EAS) AF: 0.138 AC: 709 AN: 5124

South Asian (SAS) AF: 0.199 AC: 959 AN: 4822

European-Finnish (FIN) AF: 0.258 AC: 2733 AN: 10576

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20551 AN: 67860

Other (OTH) AF: 0.259 AC: 546 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11509435; hg19: chr10-106014764;