Variant 11-67586499-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000398606.10(GSTP1):c.555T>C(p.Ser185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,613,388 control chromosomes in the GnomAD database, including 104,195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11609 hom., cov: 33)

Exomes 𝑓: 0.35 ( 92586 hom. )

Consequence

GSTP1
ENST00000398606.10 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.935

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 11-67586499-T-C is Benign according to our data. Variant chr11-67586499-T-C is described in ClinVar as [Benign]. Clinvar id is 1281843.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.935 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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.555T>C	p.Ser185=	synonymous_variant	7/7	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.555T>C	p.Ser185=	synonymous_variant	7/7	1	NM_000852.4	ENSP00000381607	P1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57622

AN:

152076

Hom.:

11594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.488

Gnomad AMI

AF:

0.380

Gnomad AMR

AF:

0.430

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.371

GnomAD3 exomes

AF:

0.346

AC:

86223

AN:

249046

Hom.:

16434

AF XY:

0.334

AC XY:

45198

AN XY:

135140

show subpopulations

Gnomad AFR exome

AF:

0.495

Gnomad AMR exome

AF:

0.528

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.176

Gnomad SAS exome

AF:

0.261

Gnomad FIN exome

AF:

0.281

Gnomad NFE exome

AF:

0.345

Gnomad OTH exome

AF:

0.345

GnomAD4 exome

AF:

0.350

AC:

511957

AN:

1461194

Hom.:

92586

Cov.:

AF XY:

0.346

AC XY:

251352

AN XY:

726954

show subpopulations

Gnomad4 AFR exome

AF:

0.497

Gnomad4 AMR exome

AF:

0.517

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.263

Gnomad4 FIN exome

AF:

0.285

Gnomad4 NFE exome

AF:

0.359

Gnomad4 OTH exome

AF:

0.343

GnomAD4 genome

AF:

0.379

AC:

57676

AN:

152194

Hom.:

11609

Cov.:

AF XY:

0.371

AC XY:

27600

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.177

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.351

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.351

Hom.:

11614

Bravo

AF:

0.401

Asia WGS

AF:

0.260

AC:

906

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 09, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.62

DANN

Benign

0.26

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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