10-104255006-CCGG-CCGGCGG

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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

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 Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTO1	NM_004832.3	c.34+49_34+51dupGGC		intron_variant	Intron 1 of 5	ENST00000369713.10	NP_004823.1
GSTO1	NM_001191003.2	c.-50-152_-50-150dupGGC		intron_variant	Intron 1 of 5		NP_001177932.1
GSTO1	NM_001191002.2	c.34+49_34+51dupGGC		intron_variant	Intron 1 of 4		NP_001177931.1
LOC124902497	XR_007062284.1	n.366-6417_366-6415dupCCG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO1	ENST00000369713.10	c.34+49_34+51dupGGC		intron_variant	Intron 1 of 5	1	NM_004832.3	ENSP00000358727.5

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-106014764;