rs34400162

Variant names:

• chr10-104275312-G-A
• rs34400162
• NM_183239.2:c.121G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-104275312-G-A
• chr10-104275312-G-C
• chr10-104275312-G-T

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The NM_183239.2(GSTO2):​c.121G>A​(p.Val41Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,613,956 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0017 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00031 (5 hom.)
• Consequence: GSTO2 NM_183239.2 missense
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 2.47
• Publications: 6 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: Benign. The variant received -16 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.014940411).
• BP6: Variant 10-104275312-G-A is Benign according to our data. Variant chr10-104275312-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 780890.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAdExome4 at 5 AR gene

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	NM_183239.2	MANE Select	c.121G>A	p.Val41Ile	missense	Exon 3 of 7	NP_899062.1
	GSTO2	NM_001191014.2		c.37G>A	p.Val13Ile	missense	Exon 1 of 5	NP_001177943.1
	GSTO2	NM_001191013.2		c.121G>A	p.Val41Ile	missense	Exon 3 of 6	NP_001177942.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTO2	ENST00000338595.7	TSL:1 MANE Select	c.121G>A	p.Val41Ile	missense	Exon 3 of 7	ENSP00000345023.1
	GSTO2	ENST00000369707.2	TSL:1	c.37G>A	p.Val13Ile	missense	Exon 1 of 5	ENSP00000358721.1
	GSTO2	ENST00000450629.6	TSL:5	c.121G>A	p.Val41Ile	missense	Exon 3 of 6	ENSP00000390986.2

Frequencies

GnomAD3 genomes AF: 0.00170 AC: 259 AN: 152102 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00572

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000590

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00191

GnomAD2 exomes AF: 0.000561 AC: 141 AN: 251280 AF XY: 0.000412

Gnomad AFR exome AF: 0.00560

Gnomad AMR exome AF: 0.000376

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000141

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.000311 AC: 454 AN: 1461736 Hom.: 5 Cov.: 31 AF XY: 0.000323 AC XY: 235 AN XY: 727194

African (AFR) AF: 0.00777 AC: 260 AN: 33472

American (AMR) AF: 0.000336 AC: 15 AN: 44706

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26124

East Asian (EAS) AF: 0.00 AC: 0 AN: 39684

South Asian (SAS) AF: 0.000255 AC: 22 AN: 86252

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53400

Middle Eastern (MID) AF: 0.00330 AC: 19 AN: 5766

European-Non Finnish (NFE) AF: 0.0000630 AC: 70 AN: 1111940

Other (OTH) AF: 0.00113 AC: 68 AN: 60392

GnomAD4 genome AF: 0.00171 AC: 260 AN: 152220 Hom.: 0 Cov.: 32 AF XY: 0.00152 AC XY: 113 AN XY: 74424

African (AFR) AF: 0.00571 AC: 237 AN: 41534

American (AMR) AF: 0.000589 AC: 9 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 68016

Other (OTH) AF: 0.00189 AC: 4 AN: 2112

Alfa AF: 0.000698 Hom.: 0

Bravo AF: 0.00191

ESP6500AA AF: 0.00545 AC: 24

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000535 AC: 65

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.000218

EpiControl AF: 0.000237

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	19
DANN	Uncertain	1.0
DEOGEN2	Benign	0.036	T
Eigen	Benign	0.16
Eigen_PC	Benign	0.16
FATHMM_MKL	Benign	0.72	D
LIST_S2	Uncertain	0.86	D
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.015	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.6	M
PhyloP100		2.5
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.90	N
REVEL	Benign	0.15
Sift	Benign	0.039	D
Sift4G	Uncertain	0.034	D
Polyphen		0.50	P
Vest4		0.24
MVP		0.36
MPC		0.095
ClinPred		0.025	T
GERP RS		4.7
PromoterAI		-0.058	Neutral
Varity_R		0.22
gMVP		0.54
Mutation Taster		=84/16	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: rs34400162; hg19: chr10-106035070;