rs8192100

Variant names:

• chr4-139695829-A-C
• rs8192100
• NM_002413.5:c.229+562A>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.229+562A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,220 control chromosomes in the GnomAD database, including 1,144 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 0.12 (1144 hom., cov: 32)
• Consequence: MGST2 NM_002413.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 7 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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGST2	NM_002413.5	c.229+562A>C		intron_variant	Intron 3 of 4	ENST00000265498.6	NP_002404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGST2	ENST00000265498.6	c.229+562A>C		intron_variant	Intron 3 of 4	1	NM_002413.5	ENSP00000265498.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18268 AN: 152102 Hom.: 1144 Cov.: 32

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.120 AC: 18274 AN: 152220 Hom.: 1144 Cov.: 32 AF XY: 0.118 AC XY: 8760 AN XY: 74422

African (AFR) AF: 0.0890 AC: 3698 AN: 41530

American (AMR) AF: 0.121 AC: 1846 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3472

East Asian (EAS) AF: 0.0903 AC: 467 AN: 5170

South Asian (SAS) AF: 0.128 AC: 616 AN: 4820

European-Finnish (FIN) AF: 0.0999 AC: 1059 AN: 10600

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9613 AN: 68006

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.137 Hom.: 2732

Bravo AF: 0.121

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.9
DANN	Benign	0.82
PhyloP100		0.029
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: rs8192100; hg19: chr4-140616983;