Variant chr12-16360227-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020300.5(MGST1):c.221+2528G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 475,272 control chromosomes in the GnomAD database, including 103,879 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.59 ( 28002 hom., cov: 31)

Exomes 𝑓: 0.68 ( 75877 hom. )

Consequence

MGST1
NM_020300.5 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.596

Variant links:

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]

MGST1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGST1	NM_020300.5 linkuse as main transcript	c.221+2528G>C		intron_variant		ENST00000396210.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGST1	ENST00000396210.8 linkuse as main transcript	c.221+2528G>C		intron_variant		1	NM_020300.5	P1	P10620-1

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

89906

AN:

151846

Hom.:

27981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.661

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.696

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.677

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.692

Gnomad OTH

AF:

0.602

GnomAD4 exome

AF:

0.682

AC:

220492

AN:

323306

Hom.:

75877

AF XY:

0.683

AC XY:

105200

AN XY:

154052

show subpopulations

Gnomad4 AFR exome

AF:

0.447

Gnomad4 AMR exome

AF:

0.489

Gnomad4 ASJ exome

AF:

0.694

Gnomad4 EAS exome

AF:

0.184

Gnomad4 SAS exome

AF:

0.550

Gnomad4 FIN exome

AF:

0.648

Gnomad4 NFE exome

AF:

0.693

Gnomad4 OTH exome

AF:

0.649

GnomAD4 genome

AF:

0.592

AC:

89967

AN:

151966

Hom.:

28002

Cov.:

AF XY:

0.588

AC XY:

43630

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.696

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.677

Gnomad4 NFE

AF:

0.692

Gnomad4 OTH

AF:

0.602

Alfa

AF:

0.648

Hom.:

16625

Bravo

AF:

0.575

Asia WGS

AF:

0.351

AC:

1222

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Pulmonary disease, chronic obstructive, susceptibility to

Other:1

association, no assertion criteria provided

research

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Jul 05, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.0

DANN

Benign

0.59

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over