Variant rs11875 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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.51

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 -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/exons	MANE	UniProt
MGST1	NM_020300.5 linkuse as main transcript	c.*19G>A		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.*19G>A		3_prime_UTR_variant	4/4	1	NM_020300.5	P1	P10620-1

Frequencies

GnomAD3 genomes

AF:

0.0705

AC:

10720

AN:

152128

Hom.:

536

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.0936

AC:

21149

AN:

225968

Hom.:

1242

AF XY:

0.0926

AC XY:

11315

AN XY:

122154

show subpopulations

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 SAS exome

AF:

0.0864

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.:

AF XY:

0.0842

AC XY:

59122

AN XY:

701928

show subpopulations

Gnomad4 AFR exome

AF:

0.0129

Gnomad4 AMR exome

AF:

0.124

Gnomad4 ASJ exome

AF:

0.0396

Gnomad4 EAS exome

AF:

0.269

Gnomad4 SAS exome

AF:

0.0836

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.0785

Gnomad4 OTH exome

AF:

0.0831

GnomAD4 genome

AF:

0.0705

AC:

10731

AN:

152246

Hom.:

538

Cov.:

AF XY:

0.0727

AC XY:

5415

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0173

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.0822

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0786

Gnomad4 OTH

AF:

0.0777

Alfa

AF:

0.0782

Hom.:

1078

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over