Variant 11-67584303-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

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

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.944

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:

GSTP1 (HGNC:):

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=-0.84).

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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
GSTP1	NM_000852.4 linkuse as main transcript	c.37+134C>T		intron_variant		ENST00000398606.10	NP_000843.1	P09211V9HWE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTP1	ENST00000398606.10 linkuse as main transcript	c.37+134C>T		intron_variant		1	NM_000852.4	ENSP00000381607.3		P09211

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48268

AN:

151792

Hom.:

8592

Cov.:

show subpopulations

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.:

AF XY:

0.382

AC XY:

120092

AN XY:

314494

show subpopulations

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.:

AF XY:

0.308

AC XY:

22894

AN XY:

74244

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

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