chr10-104279427-A-C

Variant names:

• chr10-104279427-A-C
• rs156697
• NM_183239.2:c.424A>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_183239.2(GSTO2):​c.424A>C​(p.Asn142His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: GSTO2 NM_183239.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 0 publications found

Genes affected

GSTO2 (HGNC:23064): (glutathione S-transferase omega 2) The protein encoded by this gene is an omega class glutathione S-transferase (GST). GSTs are involved in the metabolism of xenobiotics and carcinogens. Four transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09813258).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183239.2. 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
	GSTO2	NM_183239.2	MANE Select	c.424A>C	p.Asn142His	missense	Exon 5 of 7	NP_899062.1	Q9H4Y5-1
	GSTO2	NM_001191014.2		c.340A>C	p.Asn114His	missense	Exon 3 of 5	NP_001177943.1	Q9H4Y5-3
	GSTO2	NM_001191013.2		c.366+1311A>C		intron	N/A	NP_001177942.1	Q9H4Y5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	ENST00000338595.7	TSL:1 MANE Select	c.424A>C	p.Asn142His	missense	Exon 5 of 7	ENSP00000345023.1	Q9H4Y5-1
	GSTO2	ENST00000369707.2	TSL:1	c.340A>C	p.Asn114His	missense	Exon 3 of 5	ENSP00000358721.1	Q9H4Y5-3
	GSTO2	ENST00000912037.1		c.424A>C	p.Asn142His	missense	Exon 5 of 7	ENSP00000582096.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Uncertain	0.98
DEOGEN2	Benign	0.051	T
Eigen	Benign	-0.86
Eigen_PC	Benign	-0.83
FATHMM_MKL	Benign	0.028	N
LIST_S2	Benign	0.20	T
M_CAP	Benign	0.0091	T
MetaRNN	Benign	0.098	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.90	L
PhyloP100		0.57
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.90	N
REVEL	Benign	0.055
Sift	Benign	0.045	D
Sift4G	Benign	0.11	T
Polyphen		0.23	B
Vest4		0.17
MutPred		0.27		Loss of ubiquitination at K144 (P = 0.121)
MVP		0.34
MPC		0.13
ClinPred		0.21	T
GERP RS		4.0
Varity_R		0.25
gMVP		0.26
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs156697; hg19: chr10-106039185;