Variant chr11-67584785-C-A 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.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

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0150

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
GSTP1	NM_000852.4 linkuse as main transcript	c.232+13C>A		intron_variant		ENST00000398606.10	NP_000843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTP1	ENST00000398606.10 linkuse as main transcript	c.232+13C>A		intron_variant		1	NM_000852.4	ENSP00000381607	P1

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57339

AN:

151892

Hom.:

11284

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.405

AC XY:

289469

AN XY:

715478

show subpopulations

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.:

AF XY:

0.366

AC XY:

27206

AN XY:

74320

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.83

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

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