rs36209763

Variant names:

• chr1-109686330-A-G
• rs36209763
• ENST00000369831.6:c.567+14747A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000369831.6(GSTM2):​c.567+14747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (4461 hom., cov: 11)
• Consequence: GSTM2 ENST00000369831.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

Genes affected

GSTM2 (HGNC:4634): (glutathione S-transferase mu 2) Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-transferase that belongs to the mu class. The mu class of enzymes functions in the detoxification of electrophilic compounds, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress, by conjugation with glutathione. The genes encoding the mu class of enzymes are organized in a gene cluster on chromosome 1p13.3 and are known to be highly polymorphic. These genetic variations can change an individual's susceptibility to carcinogens and toxins as well as affect the toxicity and efficacy of certain drugs. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000369831.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTM2	ENST00000369831.6	TSL:2	c.567+14747A>G		intron	N/A	ENSP00000358846.2	F6XZQ7
	GSTM2	ENST00000460717.8	TSL:2	c.*17+4496A>G		intron	N/A	ENSP00000435910.2	P28161-2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 10580 AN: 80916 Hom.: 4462 Cov.: 11

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00243

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.160

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.131 AC: 10578 AN: 81036 Hom.: 4461 Cov.: 11 AF XY: 0.126 AC XY: 4973 AN XY: 39384

African (AFR) AF: 0.0229 AC: 658 AN: 28722

American (AMR) AF: 0.112 AC: 865 AN: 7706

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 475 AN: 1780

East Asian (EAS) AF: 0.00242 AC: 5 AN: 2062

South Asian (SAS) AF: 0.0836 AC: 222 AN: 2654

European-Finnish (FIN) AF: 0.180 AC: 953 AN: 5306

Middle Eastern (MID) AF: 0.235 AC: 31 AN: 132

European-Non Finnish (NFE) AF: 0.229 AC: 7153 AN: 31220

Other (OTH) AF: 0.162 AC: 173 AN: 1070

Alfa AF: 0.0954 Hom.: 478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.69
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs36209763; hg19: chr1-110228952;