11-67584785-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000852.4(GSTP1):c.232+13C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,586,772 control chromosomes in the GnomAD database, including 134,514 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.38 (11286 hom., cov: 33)
  • Exomes 𝑓: 0.41 (123228 hom.)
• Consequence: GSTP1 NM_000852.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0150

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 11-67584785-C-A is Benign according to our data. Variant chr11-67584785-C-A is described in ClinVar as [Benign]. Clinvar id is 1297979.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTP1	NM_000852.4	c.232+13C>A		intron_variant		ENST00000398606.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTP1	ENST00000398606.10	c.232+13C>A		intron_variant		1	NM_000852.4	P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57339 AN: 151892 Hom.: 11284 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.375

GnomAD3 exomes AF: 0.343 AC: 84038 AN: 245268 Hom.: 15587 AF XY: 0.349 AC XY: 46581 AN XY: 133504

Gnomad AFR exome AF: 0.395

Gnomad AMR exome AF: 0.219

Gnomad ASJ exome AF: 0.255

Gnomad EAS exome AF: 0.156

Gnomad SAS exome AF: 0.314

Gnomad FIN exome AF: 0.333

Gnomad NFE exome AF: 0.421

Gnomad OTH exome AF: 0.367

GnomAD4 exome AF: 0.407 AC: 583959 AN: 1434762 Hom.: 123228 Cov.: 28 AF XY: 0.405 AC XY: 289469 AN XY: 715478

Gnomad4 AFR exome AF: 0.390

Gnomad4 AMR exome AF: 0.225

Gnomad4 ASJ exome AF: 0.259

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.341

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.387

GnomAD4 genome AF: 0.377 AC: 57364 AN: 152010 Hom.: 11286 Cov.: 33 AF XY: 0.366 AC XY: 27206 AN XY: 74320

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.372

Alfa AF: 0.295 Hom.: 1150

Bravo AF: 0.375

Asia WGS AF: 0.254 AC: 887 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.7
Dann	Benign	0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs762803; hg19: chr11-67352256; COSMIC: COSV66992242; COSMIC: COSV66992242;