rs36210087

Positions:

• chr1-109686291-C-G
• chr1-109686291-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000369831.6(GSTM2):​c.567+14708C>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 0.056 (1729 hom., cov: 12)
• Consequence: GSTM2 ENST00000369831.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTM2	ENST00000369831.6	c.567+14708C>G		intron_variant		2
GSTM2	ENST00000460717.7	c.*17+4457C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 4415 AN: 78358 Hom.: 1727 Cov.: 12

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0335

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0477

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0614

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

GnomAD4 genome AF: 0.0563 AC: 4421 AN: 78474 Hom.: 1729 Cov.: 12 AF XY: 0.0553 AC XY: 2112 AN XY: 38172

Gnomad4 AFR AF: 0.0345

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0477

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.0612

Alfa AF: 0.0360 Hom.: 166

Asia WGS AF: 0.0260 AC: 68 AN: 2638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36210087; hg19: chr1-110228913;