NM_004832.3:c.34+49_34+51dupGGC

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_004832.3(GSTO1):​c.34+49_34+51dupGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 26)
• Consequence: GSTO1 NM_004832.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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+51dupGGC		intron	N/A	NP_004823.1	P78417-1
	GSTO1	NM_001191003.2		c.-50-152_-50-150dupGGC		intron	N/A	NP_001177932.1	P78417-3
	GSTO1	NM_001191002.2		c.34+49_34+51dupGGC		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+51dupGGC		intron	N/A	ENSP00000358727.5	P78417-1
	GSTO1	ENST00000445155.5	TSL:2	c.-202_-200dupGGC		5_prime_UTR	Exon 1 of 5	ENSP00000406708.1	Q5TA02
	GSTO1	ENST00000539281.5	TSL:5	c.-50-152_-50-150dupGGC		intron	N/A	ENSP00000441488.1	P78417-3

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs11509435; hg19: chr10-106014764;