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GeneBe

4-139695263-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_002413.5(MGST2):c.225C>T(p.Asn75=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00472 in 1,607,104 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 23 hom. )

Consequence

MGST2
NM_002413.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.257
Variant links:
Genes affected
MGST2 (HGNC:7063): (microsomal glutathione S-transferase 2) The MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism) family consists of six human proteins, several of which are involved in the production of leukotrienes and prostaglandin E, important mediators of inflammation. This gene encodes a protein which catalyzes the conjugation of leukotriene A4 and reduced glutathione to produce leukotriene C4. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 4-139695263-C-T is Benign according to our data. Variant chr4-139695263-C-T is described in ClinVar as [Benign]. Clinvar id is 710321.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.257 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MGST2NM_002413.5 linkuse as main transcriptc.225C>T p.Asn75= synonymous_variant 3/5 ENST00000265498.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MGST2ENST00000265498.6 linkuse as main transcriptc.225C>T p.Asn75= synonymous_variant 3/51 NM_002413.5 P1Q99735-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00290
AC:
441
AN:
151978
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000942
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00236
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.00152
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00497
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00329
AC:
826
AN:
251412
Hom.:
2
AF XY:
0.00336
AC XY:
456
AN XY:
135886
show subpopulations
Gnomad AFR exome
AF:
0.000738
Gnomad AMR exome
AF:
0.00133
Gnomad ASJ exome
AF:
0.000397
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00127
Gnomad FIN exome
AF:
0.00176
Gnomad NFE exome
AF:
0.00590
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00491
AC:
7142
AN:
1455008
Hom.:
23
Cov.:
28
AF XY:
0.00487
AC XY:
3528
AN XY:
724448
show subpopulations
Gnomad4 AFR exome
AF:
0.000720
Gnomad4 AMR exome
AF:
0.00130
Gnomad4 ASJ exome
AF:
0.000421
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00115
Gnomad4 FIN exome
AF:
0.00213
Gnomad4 NFE exome
AF:
0.00599
Gnomad4 OTH exome
AF:
0.00344
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00290
AC:
441
AN:
152096
Hom.:
2
Cov.:
32
AF XY:
0.00262
AC XY:
195
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.000940
Gnomad4 AMR
AF:
0.00236
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00152
Gnomad4 NFE
AF:
0.00497
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00465
Hom.:
7
Bravo
AF:
0.00295
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.00671
EpiControl
AF:
0.00581

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 17, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
Cadd
Benign
4.4
Dann
Benign
0.80
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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.

Other links and lift over

dbSNP: rs8192098; hg19: chr4-140616417; API