Variant rs8191439 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.-18G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0253 in 743,180 control chromosomes in the GnomAD database, including 2,537 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 375 hom., cov: 33)

Exomes 𝑓: 0.025 ( 2162 hom. )

Consequence

GSTP1
NM_000852.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.307

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 11-67583826-G-A is Benign according to our data. Variant chr11-67583826-G-A is described in ClinVar as [Benign]. Clinvar id is 1246555.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.175 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.-18G>A		5_prime_UTR_variant	1/7	ENST00000398606.10	NP_000843.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
GSTP1	ENST00000398606.10 linkuse as main transcript	c.-18G>A	5_prime_UTR_variant	1/7	1	NM_000852.4	ENSP00000381607	P1
GSTP1	ENST00000398603.6 linkuse as main transcript	c.-18G>A	5_prime_UTR_variant	1/6	3		ENSP00000381604
GSTP1	ENST00000494593.1 linkuse as main transcript	n.5G>A	non_coding_transcript_exon_variant	1/3	2
GSTP1	ENST00000646888.1 linkuse as main transcript		upstream_gene_variant				ENSP00000494477

Frequencies

GnomAD3 genomes

AF:

0.0265

AC:

4041

AN:

152208

Hom.:

373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0199

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.0260

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.000376

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00329

Gnomad OTH

AF:

0.0249

GnomAD3 exomes

AF:

0.0564

AC:

10302

AN:

182528

Hom.:

1717

AF XY:

0.0421

AC XY:

4234

AN XY:

100680

show subpopulations

Gnomad AFR exome

AF:

0.0194

Gnomad AMR exome

AF:

0.324

Gnomad ASJ exome

AF:

0.00838

Gnomad EAS exome

AF:

0.0231

Gnomad SAS exome

AF:

0.000633

Gnomad FIN exome

AF:

0.000376

Gnomad NFE exome

AF:

0.00300

Gnomad OTH exome

AF:

0.0367

GnomAD4 exome

AF:

0.0250

AC:

14767

AN:

590862

Hom.:

2162

Cov.:

AF XY:

0.0199

AC XY:

6391

AN XY:

321004

show subpopulations

Gnomad4 AFR exome

AF:

0.0186

Gnomad4 AMR exome

AF:

0.308

Gnomad4 ASJ exome

AF:

0.00919

Gnomad4 EAS exome

AF:

0.0124

Gnomad4 SAS exome

AF:

0.000707

Gnomad4 FIN exome

AF:

0.000868

Gnomad4 NFE exome

AF:

0.00349

Gnomad4 OTH exome

AF:

0.0210

GnomAD4 genome

AF:

0.0266

AC:

4046

AN:

152318

Hom.:

375

Cov.:

AF XY:

0.0292

AC XY:

2174

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0198

Gnomad4 AMR

AF:

0.181

Gnomad4 ASJ

AF:

0.00778

Gnomad4 EAS

AF:

0.0261

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000376

Gnomad4 NFE

AF:

0.00329

Gnomad4 OTH

AF:

0.0246

Alfa

AF:

0.00720

Hom.:

Bravo

AF:

0.0436

Asia WGS

AF:

0.0230

AC:

AN:

3472

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

-0.74

CADD

Benign

8.5

DANN

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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