Variant 12-16364098-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_020300.5(MGST1):c.*57T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 1,521,860 control chromosomes in the GnomAD database, including 5,158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

Frequency

Genomes: 𝑓 0.097 ( 1345 hom., cov: 33)

Exomes 𝑓: 0.036 ( 3813 hom. )

Consequence

MGST1
NM_020300.5 3_prime_UTR

Scores

Clinical Significance

protective no assertion criteria provided B:1

Conservation

PhyloP100: 0.536

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 12-16364098-T-G is Benign according to our data. Variant chr12-16364098-T-G is described in ClinVar as [protective]. Clinvar id is 1693601.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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.*57T>G		3_prime_UTR_variant	4/4	ENST00000396210.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGST1	ENST00000396210.8 linkuse as main transcript	c.*57T>G		3_prime_UTR_variant	4/4	1	NM_020300.5	P1	P10620-1

Frequencies

GnomAD3 genomes

AF:

0.0973

AC:

14794

AN:

152114

Hom.:

1341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0925

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0496

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0134

Gnomad OTH

AF:

0.0933

GnomAD4 exome

AF:

0.0363

AC:

49742

AN:

1369628

Hom.:

3813

Cov.:

AF XY:

0.0365

AC XY:

24548

AN XY:

672920

show subpopulations

Gnomad4 AFR exome

AF:

0.215

Gnomad4 AMR exome

AF:

0.210

Gnomad4 ASJ exome

AF:

0.0952

Gnomad4 EAS exome

AF:

0.267

Gnomad4 SAS exome

AF:

0.0908

Gnomad4 FIN exome

AF:

0.0518

Gnomad4 NFE exome

AF:

0.0105

Gnomad4 OTH exome

AF:

0.0605

GnomAD4 genome

AF:

0.0973

AC:

14809

AN:

152232

Hom.:

1345

Cov.:

AF XY:

0.101

AC XY:

7482

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.145

Gnomad4 ASJ

AF:

0.0925

Gnomad4 EAS

AF:

0.277

Gnomad4 SAS

AF:

0.102

Gnomad4 FIN

AF:

0.0496

Gnomad4 NFE

AF:

0.0134

Gnomad4 OTH

AF:

0.0961

Alfa

AF:

0.0376

Hom.:

467

Bravo

AF:

0.112

Asia WGS

AF:

0.211

AC:

735

AN:

3478

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Pulmonary disease, chronic obstructive, susceptibility to

Benign:1

protective, no assertion criteria provided

research

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Jul 05, 2022

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.0

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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