ENST00000414179.6:c.256-1042A>G

Variant names:

• chr1-109680767-A-G
• rs535088
• ENST00000414179.6:c.256-1042A>G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTM2	NM_001142368.2	c.568-1042A>G		intron_variant	Intron 7 of 8		NP_001135840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTM2	ENST00000414179.6	c.256-1042A>G		intron_variant	Intron 7 of 8	1		ENSP00000404662.2
GSTM2	ENST00000369831.6	c.567+9184A>G		intron_variant	Intron 7 of 7	2		ENSP00000358846.2
GSTM2	ENST00000442650.5	c.568-1042A>G		intron_variant	Intron 7 of 8	5		ENSP00000416883.1
GSTM2	ENST00000460717.8	c.568-1042A>G		intron_variant	Intron 7 of 8	2		ENSP00000435910.2

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

African (AFR) AF: 0.543 AC: 705 AN: 1298

American (AMR) AF: 0.780 AC: 284 AN: 364

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 59 AN: 78

East Asian (EAS) AF: 0.964 AC: 108 AN: 112

South Asian (SAS) AF: 0.725 AC: 129 AN: 178

European-Finnish (FIN) AF: 0.759 AC: 85 AN: 112

Middle Eastern (MID) AF: 0.636 AC: 14 AN: 22

European-Non Finnish (NFE) AF: 0.823 AC: 1219 AN: 1482

Other (OTH) AF: 0.675 AC: 54 AN: 80

Alfa AF: 0.00 Hom.: 0

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
PhyloP100		1.3
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: rs535088; hg19: chr1-110223389;