rs10772939

Variant names:

• chr12-16456104-T-C
• rs10772939
• ENST00000538857.1:n.482+72500T>C

Variant summary

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

The ENST00000538857.1(MGST1):​n.482+72500T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,624 control chromosomes in the GnomAD database, including 13,465 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 0.39 (13465 hom., cov: 32)
• Consequence: MGST1 ENST00000538857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 5 publications found

Genes affected

MGST1 (HGNC:7061): (microsomal glutathione S-transferase 1) The MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism) family consists of six human proteins, two of which are involved in the production of leukotrienes and prostaglandin E, important mediators of inflammation. Other family members, demonstrating glutathione S-transferase and peroxidase activities, are involved in cellular defense against toxic, carcinogenic, and pharmacologically active electrophilic compounds. This gene encodes a protein that catalyzes the conjugation of glutathione to electrophiles and the reduction of lipid hydroperoxides. This protein is localized to the endoplasmic reticulum and outer mitochondrial membrane where it is thought to protect these membranes from oxidative stress. Several transcript variants, some non-protein coding and some protein coding, have been found for this gene. [provided by RefSeq, May 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000538857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGST1	ENST00000538857.1	TSL:3	n.482+72500T>C		intron	N/A
	MGST1	ENST00000539036.5	TSL:4	n.400+72500T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59081 AN: 151504 Hom.: 13463 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.390 AC: 59102 AN: 151624 Hom.: 13465 Cov.: 32 AF XY: 0.388 AC XY: 28722 AN XY: 74064

African (AFR) AF: 0.137 AC: 5676 AN: 41486

American (AMR) AF: 0.434 AC: 6598 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1909 AN: 5134

South Asian (SAS) AF: 0.490 AC: 2358 AN: 4816

European-Finnish (FIN) AF: 0.451 AC: 4734 AN: 10508

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 34987 AN: 67700

Other (OTH) AF: 0.418 AC: 880 AN: 2104

Alfa AF: 0.473 Hom.: 41684

Bravo AF: 0.378

Asia WGS AF: 0.396 AC: 1369 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.42
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10772939; hg19: chr12-16609038;