ENST00000369831.6:c.567+14708C>G

Variant names:

• chr1-109686291-C-G
• rs36210087
• ENST00000369831.6:c.567+14708C>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+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
• Publications: 2 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=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTM2	ENST00000369831.6	c.567+14708C>G		intron_variant	Intron 7 of 7	2		ENSP00000358846.2
GSTM2	ENST00000460717.8	c.*17+4457C>G		intron_variant	Intron 8 of 8	2		ENSP00000435910.2

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

African (AFR) AF: 0.0345 AC: 983 AN: 28492

American (AMR) AF: 0.167 AC: 1230 AN: 7386

Ashkenazi Jewish (ASJ) AF: 0.0477 AC: 80 AN: 1676

East Asian (EAS) AF: 0.0303 AC: 57 AN: 1884

South Asian (SAS) AF: 0.0236 AC: 61 AN: 2588

European-Finnish (FIN) AF: 0.0238 AC: 118 AN: 4958

Middle Eastern (MID) AF: 0.0323 AC: 4 AN: 124

European-Non Finnish (NFE) AF: 0.0605 AC: 1812 AN: 29948

Other (OTH) AF: 0.0612 AC: 63 AN: 1030

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
PhyloP100		1.6
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs36210087; hg19: chr1-110228913;