rs535088

Positions:

• chr1-109680767-A-G
• chr1-109680767-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000414179.6(GSTM2):​c.256-1042A>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 0.71 (1031 hom., cov: 3)
  • Failed GnomAD Quality Control
• Consequence: GSTM2 ENST00000414179.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTM2	NM_001142368.2	c.568-1042A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTM2	ENST00000414179.6	c.256-1042A>G		intron_variant		1
GSTM2	ENST00000369831.6	c.567+9184A>G		intron_variant		2
GSTM2	ENST00000442650.5	c.568-1042A>G		intron_variant		5
GSTM2	ENST00000460717.7	c.568-1042A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 2673 AN: 3748 Hom.: 1032 Cov.: 3

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.625

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.683

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.713 AC: 2672 AN: 3748 Hom.: 1031 Cov.: 3 AF XY: 0.717 AC XY: 1183 AN XY: 1650

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs535088; hg19: chr1-110223389;