1-109687481-C-T

Position:

• chr1-109687481-C-T

Variant summary

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

The ENST00000369831.6(GSTM2):​c.567+15898C>T 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 0.22 (5124 hom., cov: 16)
• Consequence: GSTM2 ENST00000369831.6 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]

(HGNC:):

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 = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109687481C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTM2	ENST00000369831.6	c.567+15898C>T		intron_variant		2		ENSP00000358846.2
GSTM2	ENST00000460717.7	c.*17+5647C>T		intron_variant		2		ENSP00000435910.2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 23508 AN: 107634 Hom.: 5119 Cov.: 16

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.219 AC: 23544 AN: 107748 Hom.: 5124 Cov.: 16 AF XY: 0.220 AC XY: 11504 AN XY: 52232

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.233

Alfa AF: 0.149 Hom.: 504

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	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4147563; hg19: chr1-110230103;