1-109687334-C-G

Variant names:

• chr1-109687334-C-G
• rs3815029
• ENST00000369831.6:c.567+15751C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000369831.6(GSTM2):​c.567+15751C>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 0.22 (2695 hom., cov: 9)
  • Failed GnomAD Quality Control
• Consequence: GSTM2 ENST00000369831.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 4 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=-0.9).

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+15751C>G		intron_variant	Intron 7 of 7	2		ENSP00000358846.2
GSTM2	ENST00000460717.8	c.*17+5500C>G		intron_variant	Intron 8 of 8	2		ENSP00000435910.2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 13808 AN: 62724 Hom.: 2695 Cov.: 9

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.238

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: 0.220 AC: 13816 AN: 62788 Hom.: 2695 Cov.: 9 AF XY: 0.222 AC XY: 6715 AN XY: 30250

African (AFR) AF: 0.116 AC: 2595 AN: 22404

American (AMR) AF: 0.253 AC: 1349 AN: 5326

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 353 AN: 1412

East Asian (EAS) AF: 0.367 AC: 555 AN: 1512

South Asian (SAS) AF: 0.201 AC: 361 AN: 1792

European-Finnish (FIN) AF: 0.227 AC: 879 AN: 3876

Middle Eastern (MID) AF: 0.237 AC: 18 AN: 76

European-Non Finnish (NFE) AF: 0.295 AC: 7464 AN: 25330

Other (OTH) AF: 0.240 AC: 176 AN: 732

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	-0.90
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.59
PromoterAI		-0.098	Neutral
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: rs3815029; hg19: chr1-110229956;