NM_002413.5:c.58+1160T>C

Variant names:

• chr4-139667237-T-C
• rs8192013
• NM_002413.5:c.58+1160T>C

Variant summary

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

The NM_002413.5(MGST2):​c.58+1160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,044 control chromosomes in the GnomAD database, including 3,333 homozygotes. 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 (3333 hom., cov: 32)
• Consequence: MGST2 NM_002413.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 14 publications found

Genes affected

MGST2 (HGNC:7063): (microsomal glutathione S-transferase 2) The MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism) family consists of six human proteins, several of which are involved in the production of leukotrienes and prostaglandin E, important mediators of inflammation. This gene encodes a protein which catalyzes the conjugation of leukotriene A4 and reduced glutathione to produce leukotriene C4. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002413.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGST2	NM_002413.5	MANE Select	c.58+1160T>C		intron	N/A	NP_002404.1	Q99735-1
	MGST2	NM_001204366.2		c.58+1160T>C		intron	N/A	NP_001191295.1	Q99735-1
	MGST2	NM_001204367.2		c.-47+1160T>C		intron	N/A	NP_001191296.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGST2	ENST00000265498.6	TSL:1 MANE Select	c.58+1160T>C		intron	N/A	ENSP00000265498.1	Q99735-1
	MGST2	ENST00000515137.5	TSL:1	n.145+1160T>C		intron	N/A
	MGST2	ENST00000899649.1		c.58+1160T>C		intron	N/A	ENSP00000569708.1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30295 AN: 151928 Hom.: 3327 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.199 AC: 30318 AN: 152044 Hom.: 3333 Cov.: 32 AF XY: 0.199 AC XY: 14797 AN XY: 74318

African (AFR) AF: 0.262 AC: 10824 AN: 41380

American (AMR) AF: 0.154 AC: 2357 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1938 AN: 5160

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4818

European-Finnish (FIN) AF: 0.118 AC: 1249 AN: 10594

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11080 AN: 68024

Other (OTH) AF: 0.204 AC: 432 AN: 2114

Alfa AF: 0.179 Hom.: 4743

Bravo AF: 0.204

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.40
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8192013; hg19: chr4-140588391;