rs11875

Variant names:

• chr12-16364060-G-A
• rs11875
• NM_020300.5:c.*19G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-16364060-G-A
• chr12-16364060-G-C

Variant summary

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

The NM_020300.5(MGST1):​c.*19G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 1,570,844 control chromosomes in the GnomAD database, including 6,649 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 0.070 (538 hom., cov: 33)
  • Exomes 𝑓: 0.084 (6111 hom.)
• Consequence: MGST1 NM_020300.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 21 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGST1	NM_020300.5	c.*19G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000396210.8	NP_064696.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGST1	ENST00000396210.8	c.*19G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_020300.5	ENSP00000379513.3

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10720 AN: 152128 Hom.: 536 Cov.: 33

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.0775

GnomAD2 exomes AF: 0.0936 AC: 21149 AN: 225968 AF XY: 0.0926

Gnomad AFR exome AF: 0.0154

Gnomad AMR exome AF: 0.124

Gnomad ASJ exome AF: 0.0390

Gnomad EAS exome AF: 0.228

Gnomad FIN exome AF: 0.102

Gnomad NFE exome AF: 0.0785

Gnomad OTH exome AF: 0.0932

GnomAD4 exome AF: 0.0841 AC: 119353 AN: 1418598 Hom.: 6111 Cov.: 32 AF XY: 0.0842 AC XY: 59122 AN XY: 701928

African (AFR) AF: 0.0129 AC: 410 AN: 31824

American (AMR) AF: 0.124 AC: 4793 AN: 38682

Ashkenazi Jewish (ASJ) AF: 0.0396 AC: 943 AN: 23814

East Asian (EAS) AF: 0.269 AC: 10552 AN: 39250

South Asian (SAS) AF: 0.0836 AC: 6739 AN: 80592

European-Finnish (FIN) AF: 0.101 AC: 5250 AN: 52096

Middle Eastern (MID) AF: 0.0677 AC: 372 AN: 5496

European-Non Finnish (NFE) AF: 0.0785 AC: 85449 AN: 1088514

Other (OTH) AF: 0.0831 AC: 4845 AN: 58330

GnomAD4 genome AF: 0.0705 AC: 10731 AN: 152246 Hom.: 538 Cov.: 33 AF XY: 0.0727 AC XY: 5415 AN XY: 74434

African (AFR) AF: 0.0173 AC: 718 AN: 41576

American (AMR) AF: 0.107 AC: 1639 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3466

East Asian (EAS) AF: 0.228 AC: 1178 AN: 5174

South Asian (SAS) AF: 0.0822 AC: 396 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1088 AN: 10600

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0786 AC: 5347 AN: 68012

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0754 Hom.: 1651

Bravo AF: 0.0701

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.33
DANN	Benign	0.26
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs11875; hg19: chr12-16516994; COSMIC: COSV50566374; COSMIC: COSV50566374;