1-109687394-G-A

Position:

• chr1-109687394-G-A

Variant summary

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

The ENST00000369831.6(GSTM2):​c.567+15811G>A 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 0.36 (9467 hom., cov: 13)
• Consequence: GSTM2 ENST00000369831.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTM2	ENST00000369831.6	c.567+15811G>A		intron_variant		2		ENSP00000358846
GSTM2	ENST00000460717.7	c.*17+5560G>A		intron_variant		2		ENSP00000435910

Frequencies

GnomAD3 genomes AF: 0.360 AC: 33174 AN: 92102 Hom.: 9456 Cov.: 13

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.360 AC: 33216 AN: 92190 Hom.: 9467 Cov.: 13 AF XY: 0.356 AC XY: 15849 AN XY: 44494

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.363

Alfa AF: 0.398 Hom.: 1292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs412302; hg19: chr1-110230016;