rs412302

Variant names:

• chr1-109687394-G-A
• rs412302
• ENST00000369831.6:c.567+15811G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-109687394-G-A
• chr1-109687394-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000369831.6(GSTM2):​c.567+15811G>A 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 0.36 (9467 hom., cov: 13)
• Consequence: GSTM2 ENST00000369831.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• 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: Benign. The variant received -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 = 0.42 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+15811G>A		intron_variant	Intron 7 of 7	2		ENSP00000358846.2
GSTM2	ENST00000460717.8	c.*17+5560G>A		intron_variant	Intron 8 of 8	2		ENSP00000435910.2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 33174 AN: 92102 Hom.: 9456 Cov.: 13

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.360 AC: 33216 AN: 92190 Hom.: 9467 Cov.: 13 AF XY: 0.356 AC XY: 15849 AN XY: 44494

African (AFR) AF: 0.427 AC: 10570 AN: 24770

American (AMR) AF: 0.417 AC: 3920 AN: 9408

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 842 AN: 2224

East Asian (EAS) AF: 0.237 AC: 960 AN: 4046

South Asian (SAS) AF: 0.424 AC: 1296 AN: 3058

European-Finnish (FIN) AF: 0.236 AC: 1543 AN: 6540

Middle Eastern (MID) AF: 0.315 AC: 53 AN: 168

European-Non Finnish (NFE) AF: 0.336 AC: 13549 AN: 40382

Other (OTH) AF: 0.363 AC: 426 AN: 1174

Alfa AF: 0.398 Hom.: 1292

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	0.58
PhyloP100		-1.0
PromoterAI		-0.015	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: rs412302; hg19: chr1-110230016;