Genetic Variant MGST3:c.*282G>T (chr1-165655786-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004528.4(MGST3):c.*282G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 446,622 control chromosomes in the GnomAD database, including 19,868 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

Frequency

Genomes: 𝑓 0.24 ( 6066 hom., cov: 30)

Exomes 𝑓: 0.24 ( 13802 hom. )

Consequence

MGST3
NM_004528.4 3_prime_UTR

Scores

Clinical Significance

protective no assertion criteria provided B:1

Conservation

PhyloP100: -0.438

Publications

7 publications found

Variant links:

Genes affected

MGST3 (HGNC:7064): (microsomal glutathione S-transferase 3) This gene encodes a member of the MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism) protein family. Members of this family are involved in the production of leukotrienes and prostaglandin E, important mediators of inflammation. This gene encodes an enzyme which catalyzes the conjugation of leukotriene A4 and reduced glutathione to produce leukotriene C4. This enzyme also demonstrates glutathione-dependent peroxidase activity towards lipid hydroperoxides.[provided by RefSeq, May 2011]

MGST3 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004528.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGST3	NM_004528.4	MANE Select	c.*282G>T		3_prime_UTR	Exon 6 of 6	NP_004519.1	O14880

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MGST3	ENST00000367889.8	TSL:1 MANE Select	c.*282G>T	3_prime_UTR	Exon 6 of 6	ENSP00000356864.3	O14880
MGST3	ENST00000627653.1	TSL:5	c.*282G>T	3_prime_UTR	Exon 6 of 6	ENSP00000487151.1	Q5VV89
MGST3	ENST00000855187.1		c.*282G>T	3_prime_UTR	Exon 6 of 6	ENSP00000525246.1

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36761

AN:

151284

Hom.:

6045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.0418

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.811

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.228

GnomAD4 exome

AF:

0.244

AC:

72129

AN:

295220

Hom.:

13802

Cov.:

AF XY:

0.254

AC XY:

40131

AN XY:

158024

show subpopulations

African (AFR)

AF:

0.318

AC:

2843

AN:

8950

American (AMR)

AF:

0.439

AC:

5802

AN:

13230

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

993

AN:

8848

East Asian (EAS)

AF:

0.833

AC:

14413

AN:

17298

South Asian (SAS)

AF:

0.398

AC:

15454

AN:

38828

European-Finnish (FIN)

AF:

0.145

AC:

2094

AN:

14392

Middle Eastern (MID)

AF:

0.169

AC:

205

AN:

1216

European-Non Finnish (NFE)

AF:

0.151

AC:

26630

AN:

175894

Other (OTH)

AF:

0.223

AC:

3695

AN:

16564

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.524

Heterozygous variant carriers

2206

4412

6617

8823

11029

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

376

752

1128

1504

1880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.243

AC:

36828

AN:

151402

Hom.:

6066

Cov.:

AF XY:

0.251

AC XY:

18586

AN XY:

73924

show subpopulations

African (AFR)

AF:

0.319

AC:

13132

AN:

41184

American (AMR)

AF:

0.337

AC:

5109

AN:

15166

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

373

AN:

3470

East Asian (EAS)

AF:

0.811

AC:

4174

AN:

5146

South Asian (SAS)

AF:

0.415

AC:

1984

AN:

4780

European-Finnish (FIN)

AF:

0.148

AC:

1549

AN:

10482

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.146

AC:

9936

AN:

67862

Other (OTH)

AF:

0.230

AC:

484

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1229

2458

3688

4917

6146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.187

Hom.:

15644

Bravo

AF:

0.263

Asia WGS

AF:

0.573

AC:

1988

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:protective

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

Pulmonary disease, chronic obstructive, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.16

(source)

DANN

Benign

0.49

PhyloP100

-0.44

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over