rs36211088

Variant names:

• chr11-67583528-C-A
• rs36211088
• ENST00000398603.6:c.-316C>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.05

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]

ACMG classification

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	c.-316C>A		upstream_gene_variant		3		ENSP00000381604.1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56611 AN: 151490 Hom.: 11013 Cov.: 32

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

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.: 32 AF XY: 0.363 AC XY: 26854 AN XY: 74064

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

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

Other links and lift over

dbSNP: rs36211088; hg19: chr11-67350999;