chr1-109686677-A-G

Variant names:

• chr1-109686677-A-G
• rs36209754
• ENST00000369831.6:c.567+15094A>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+15094A>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 0.20 (6288 hom., cov: 11)
• Consequence: GSTM2 ENST00000369831.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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+15094A>G		intron_variant	Intron 7 of 7	2		ENSP00000358846.2
GSTM2	ENST00000460717.8	c.*17+4843A>G		intron_variant	Intron 8 of 8	2		ENSP00000435910.2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 15644 AN: 79742 Hom.: 6282 Cov.: 11

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.00344

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.196 AC: 15663 AN: 79858 Hom.: 6288 Cov.: 11 AF XY: 0.194 AC XY: 7524 AN XY: 38832

African (AFR) AF: 0.185 AC: 5146 AN: 27876

American (AMR) AF: 0.139 AC: 1048 AN: 7524

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 461 AN: 1750

East Asian (EAS) AF: 0.00344 AC: 7 AN: 2034

South Asian (SAS) AF: 0.193 AC: 515 AN: 2662

European-Finnish (FIN) AF: 0.180 AC: 943 AN: 5230

Middle Eastern (MID) AF: 0.336 AC: 43 AN: 128

European-Non Finnish (NFE) AF: 0.232 AC: 7247 AN: 31218

Other (OTH) AF: 0.199 AC: 207 AN: 1040

Alfa AF: 0.126 Hom.: 607

Asia WGS AF: 0.140 AC: 273 AN: 1926

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		0.35
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: rs36209754; hg19: chr1-110229299;