Genetic Variant ENST00000540992.1:n.786C>A (chr12-16514230-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000540992.1(ENSG00000256450):n.786C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 304,996 control chromosomes in the GnomAD database, including 236 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 0.0087 ( 56 hom., cov: 33)

Exomes 𝑓: 0.022 ( 180 hom. )

Consequence

ENSG00000256450
ENST00000540992.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.411

Publications

1 publications found

Variant links:

Genes affected

ENSG00000256450 (HGNC:):

ENSG00000256450 links:

GOT2P4 (HGNC:22936):

GOT2P4 links:

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:

Genome browser will be placed here

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=-0.57).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOT2P4		n.16514230C>A		intragenic_variant
MGST1	XM_047428857.1 link	c.*17-75298C>A		intron_variant	Intron 5 of 5		XP_047284813.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000256450	ENST00000540992.1 link	n.786C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
MGST1	ENST00000538857.1 link	n.483-75298C>A	intron_variant	Intron 4 of 4	3
MGST1	ENST00000539036.5 link	n.401-94864C>A	intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.00875

AC:

1332

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000700

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00871

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.0885

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000367

Gnomad OTH

AF:

0.00573

GnomAD4 exome

AF:

0.0222

AC:

3391

AN:

152722

Hom.:

180

Cov.:

AF XY:

0.0288

AC XY:

2431

AN XY:

84518

show subpopulations

African (AFR)

AF:

0.000495

AC:

AN:

4040

American (AMR)

AF:

0.0209

AC:

146

AN:

6970

Ashkenazi Jewish (ASJ)

AF:

0.000900

AC:

AN:

3332

East Asian (EAS)

AF:

0.147

AC:

815

AN:

5562

South Asian (SAS)

AF:

0.0790

AC:

2281

AN:

28866

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9320

Middle Eastern (MID)

AF:

0.00345

AC:

AN:

580

European-Non Finnish (NFE)

AF:

0.000405

AC:

AN:

86402

Other (OTH)

AF:

0.0140

AC:

107

AN:

7650

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

137

275

412

550

687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.00873

AC:

1329

AN:

152274

Hom.:

Cov.:

AF XY:

0.0109

AC XY:

809

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.000698

AC:

AN:

41566

American (AMR)

AF:

0.00883

AC:

135

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3470

East Asian (EAS)

AF:

0.136

AC:

698

AN:

5150

South Asian (SAS)

AF:

0.0883

AC:

426

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000368

AC:

AN:

68026

Other (OTH)

AF:

0.00567

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

118

176

235

294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.00158

Hom.:

Bravo

AF:

0.00793

Asia WGS

AF:

0.0920

AC:

320

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.15

(source)

DANN

Benign

0.75

PhyloP100

-0.41

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over