4-139667237-T-C

Position:

• chr4-139667237-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGST2	NM_002413.5	c.58+1160T>C		intron_variant		ENST00000265498.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGST2	ENST00000265498.6	c.58+1160T>C		intron_variant		1	NM_002413.5	P1

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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.204

Alfa AF: 0.175 Hom.: 3233

Bravo AF: 0.204

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs8192013; hg19: chr4-140588391;