1-109736350-C-T

Variant summary

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

The NM_000849.5(GSTM3):​c.*721G>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 0.549 in 151,874 control chromosomes in the GnomAD database, including 23,341 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 0.55 ( 23341 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

GSTM3
NM_000849.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.679
Variant links:
Genes affected
GSTM3 (HGNC:4635): (glutathione S-transferase mu 3) Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-transferase that belongs to the mu class. The mu class of enzymes functions in the detoxification of electrophilic compounds, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress, by conjugation with glutathione. The genes encoding the mu class of enzymes are organized in a gene cluster on chromosome 1p13.3 and are known to be highly polymorphic. These genetic variations can change an individual's susceptibility to carcinogens and toxins as well as affect the toxicity and efficacy of certain drugs. Mutations of this class mu gene have been linked with a slight increase in a number of cancers, likely due to exposure with environmental toxins. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008]
GSTM5 (HGNC:4637): (glutathione S-transferase mu 5) Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-transferase that belongs to the mu class. The mu class of enzymes functions in the detoxification of electrophilic compounds, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress, by conjugation with glutathione. The genes encoding the mu class of enzymes are organized in a gene cluster on chromosome 1p13.3 and are known to be highly polymorphic. These genetic variations can change an individual's susceptibility to carcinogens and toxins as well as affect the toxicity and efficacy of certain drugs. Diversification of these genes has occurred in regions encoding substrate-binding domains, as well as in tissue expression patterns, to accommodate an increasing number of foreign compounds. [provided by RefSeq, Jul 2008]

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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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GSTM3NM_000849.5 linkc.*721G>A 3_prime_UTR_variant 9/9 ENST00000361066.7 NP_000840.2 P21266Q6FGJ9
GSTM3NR_024537.2 linkn.1633G>A non_coding_transcript_exon_variant 8/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GSTM3ENST00000361066 linkc.*721G>A 3_prime_UTR_variant 9/91 NM_000849.5 ENSP00000354357.2 P21266
GSTM3ENST00000256594 linkc.*721G>A 3_prime_UTR_variant 8/81 ENSP00000256594.3 P21266
GSTM5ENST00000429410.2 linkn.82+24002C>T intron_variant 2
ENSG00000241720ENST00000431955.1 linkn.426-590C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.549
AC:
83245
AN:
151758
Hom.:
23313
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.595
Gnomad AMI
AF:
0.511
Gnomad AMR
AF:
0.562
Gnomad ASJ
AF:
0.445
Gnomad EAS
AF:
0.844
Gnomad SAS
AF:
0.607
Gnomad FIN
AF:
0.492
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.506
Gnomad OTH
AF:
0.523
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.549
AC:
83326
AN:
151874
Hom.:
23341
Cov.:
32
AF XY:
0.549
AC XY:
40723
AN XY:
74218
show subpopulations
Gnomad4 AFR
AF:
0.595
Gnomad4 AMR
AF:
0.563
Gnomad4 ASJ
AF:
0.445
Gnomad4 EAS
AF:
0.843
Gnomad4 SAS
AF:
0.607
Gnomad4 FIN
AF:
0.492
Gnomad4 NFE
AF:
0.506
Gnomad4 OTH
AF:
0.527
Alfa
AF:
0.506
Hom.:
12605
Bravo
AF:
0.555
Asia WGS
AF:
0.679
AC:
2355
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.92
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs1537236; hg19: chr1-110278972; API