Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000852.4(GSTP1):c.337-322G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,906 control chromosomes in the GnomAD database, including 6,808 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6808 hom., cov: 30)

Consequence

GSTP1
NM_000852.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.387

Publications

51 publications found

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 was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 11-67585782-G-A is Benign according to our data. Variant chr11-67585782-G-A is described in ClinVar as Benign. ClinVar VariationId is 1253210.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000852.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTP1	NM_000852.4	MANE Select	c.337-322G>A		intron	N/A	NP_000843.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GSTP1	ENST00000398606.10	TSL:1 MANE Select	c.337-322G>A	intron	N/A	ENSP00000381607.3
GSTP1	ENST00000398603.6	TSL:3	c.336+541G>A	intron	N/A	ENSP00000381604.1
GSTP1	ENST00000467591.1	TSL:2	n.448-322G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44379

AN:

151786

Hom.:

6800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.306

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.292

AC:

44413

AN:

151906

Hom.:

6808

Cov.:

AF XY:

0.284

AC XY:

21078

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.261

AC:

10794

AN:

41406

American (AMR)

AF:

0.223

AC:

3412

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

741

AN:

3470

East Asian (EAS)

AF:

0.153

AC:

784

AN:

5132

South Asian (SAS)

AF:

0.241

AC:

1156

AN:

4800

European-Finnish (FIN)

AF:

0.273

AC:

2896

AN:

10590

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.347

AC:

23579

AN:

67932

Other (OTH)

AF:

0.304

AC:

639

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1553

3106

4658

6211

7764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

460

920

1380

1840

2300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.319

Hom.:

11470

Bravo

AF:

0.289

Asia WGS

AF:

0.231

AC:

804

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

7.7

(source)

DANN

Benign

0.91

PhyloP100

0.39

PromoterAI

-0.019

Neutral

(source)

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

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NM_000852.4:c.337-322G>A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over