Genetic Variant GSTP1:c.-316C>A (chr11-67583528-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000398603.6(GSTP1):c.-316C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 312,834 control chromosomes in the GnomAD database, including 23,278 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 11014 hom., cov: 32)

Exomes 𝑓: 0.38 ( 12264 hom. )

Consequence

GSTP1
ENST00000398603.6 upstream_gene

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.05

Variant links:

Genes affected

GSTP1 (HGNC:4638): (glutathione S-transferase pi 1) Glutathione S-transferases (GSTs) are a family of enzymes that play an important role in detoxification by catalyzing the conjugation of many hydrophobic and electrophilic compounds with reduced glutathione. Based on their biochemical, immunologic, and structural properties, the soluble GSTs are categorized into 4 main classes: alpha, mu, pi, and theta. This GST family member is a polymorphic gene encoding active, functionally different GSTP1 variant proteins that are thought to function in xenobiotic metabolism and play a role in susceptibility to cancer, and other diseases. [provided by RefSeq, Jul 2008]

GSTP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 11-67583528-C-A is Benign according to our data. Variant chr11-67583528-C-A is described in ClinVar as [Benign]. Clinvar id is 1249154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTP1	ENST00000398603.6 link	c.-316C>A		upstream_gene_variant		3		ENSP00000381604.1		A8MX94

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56611

AN:

151490

Hom.:

11013

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.330

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.370

GnomAD4 exome

AF:

0.377

AC:

60725

AN:

161240

Hom.:

12264

AF XY:

0.379

AC XY:

31002

AN XY:

81870

show subpopulations

Gnomad4 AFR exome

AF:

0.395

Gnomad4 AMR exome

AF:

0.265

Gnomad4 ASJ exome

AF:

0.266

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.304

Gnomad4 FIN exome

AF:

0.349

Gnomad4 NFE exome

AF:

0.423

Gnomad4 OTH exome

AF:

0.373

GnomAD4 genome

AF:

0.374

AC:

56629

AN:

151594

Hom.:

11014

Cov.:

AF XY:

0.363

AC XY:

26854

AN XY:

74064

show subpopulations

Gnomad4 AFR

AF:

0.385

Gnomad4 AMR

AF:

0.277

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.157

Gnomad4 SAS

AF:

0.294

Gnomad4 FIN

AF:

0.319

Gnomad4 NFE

AF:

0.425

Gnomad4 OTH

AF:

0.367

Alfa

AF:

0.390

Hom.:

1502

Bravo

AF:

0.372

Asia WGS

AF:

0.242

AC:

829

AN:

3422

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.3

DANN

Benign

0.36

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over