11-67584303-C-T

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.37+134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 748,850 control chromosomes in the GnomAD database, including 55,712 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (8586 hom., cov: 32)
  • Exomes 𝑓: 0.38 (47126 hom.)
• Consequence: GSTP1 NM_000852.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.944

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=-0.84).
• BP6: Variant 11-67584303-C-T is Benign according to our data. Variant chr11-67584303-C-T is described in ClinVar as [Benign]. Clinvar id is 1180407.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTP1	NM_000852.4	c.37+134C>T		intron_variant		ENST00000398606.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTP1	ENST00000398606.10	c.37+134C>T		intron_variant		1	NM_000852.4	P1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48268 AN: 151792 Hom.: 8592 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.385 AC: 229669 AN: 596940 Hom.: 47126 Cov.: 8 AF XY: 0.382 AC XY: 120092 AN XY: 314494

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.232

Gnomad4 ASJ exome AF: 0.260

Gnomad4 EAS exome AF: 0.152

Gnomad4 SAS exome AF: 0.313

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.363

GnomAD4 genome AF: 0.318 AC: 48260 AN: 151910 Hom.: 8586 Cov.: 32 AF XY: 0.308 AC XY: 22894 AN XY: 74244

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.325

Alfa AF: 0.240 Hom.: 585

Bravo AF: 0.307

Asia WGS AF: 0.238 AC: 827 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.3
Dann	Benign	0.86
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2370143; hg19: chr11-67351774; COSMIC: COSV66992693; COSMIC: COSV66992693;