Genetic Variant NM_000852.4:c.37+34G>A (chr11-67584203-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_000852.4(GSTP1):c.37+34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0324 in 1,557,038 control chromosomes in the GnomAD database, including 1,027 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.026 ( 72 hom., cov: 32)

Exomes 𝑓: 0.033 ( 955 hom. )

Consequence

GSTP1
NM_000852.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283

Publications

4 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0258 (3925/152078) while in subpopulation NFE AF = 0.0379 (2573/67920). AF 95% confidence interval is 0.0367. There are 72 homozygotes in GnomAd4. There are 1945 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 72 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTP1	NM_000852.4 link	c.37+34G>A		intron_variant	Intron 2 of 6	ENST00000398606.10	NP_000843.1	P09211V9HWE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTP1	ENST00000398606.10 link	c.37+34G>A		intron_variant	Intron 2 of 6	1	NM_000852.4	ENSP00000381607.3		P09211

Frequencies

GnomAD3 genomes

AF:

0.0258

AC:

3927

AN:

151964

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00577

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0104

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.0101

Gnomad FIN

AF:

0.0711

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0379

Gnomad OTH

AF:

0.0202

GnomAD2 exomes

AF:

0.0278

AC:

6716

AN:

241730

AF XY:

0.0278

show subpopulations

Gnomad AFR exome

AF:

0.00580

Gnomad AMR exome

AF:

0.00656

Gnomad ASJ exome

AF:

0.0234

Gnomad EAS exome

AF:

0.000226

Gnomad FIN exome

AF:

0.0685

Gnomad NFE exome

AF:

0.0394

Gnomad OTH exome

AF:

0.0286

GnomAD4 exome

AF:

0.0332

AC:

46581

AN:

1404960

Hom.:

955

Cov.:

AF XY:

0.0327

AC XY:

22968

AN XY:

701734

show subpopulations

African (AFR)

AF:

0.00499

AC:

163

AN:

32694

American (AMR)

AF:

0.00688

AC:

305

AN:

44354

Ashkenazi Jewish (ASJ)

AF:

0.0252

AC:

647

AN:

25678

East Asian (EAS)

AF:

0.000152

AC:

AN:

39376

South Asian (SAS)

AF:

0.00983

AC:

835

AN:

84968

European-Finnish (FIN)

AF:

0.0696

AC:

3687

AN:

52986

Middle Eastern (MID)

AF:

0.00548

AC:

AN:

5662

European-Non Finnish (NFE)

AF:

0.0370

AC:

39282

AN:

1060872

Other (OTH)

AF:

0.0278

AC:

1625

AN:

58370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

2134

4267

6401

8534

10668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1372

2744

4116

5488

6860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0258

AC:

3925

AN:

152078

Hom.:

Cov.:

AF XY:

0.0262

AC XY:

1945

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.00576

AC:

239

AN:

41522

American (AMR)

AF:

0.0104

AC:

159

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0274

AC:

AN:

3468

East Asian (EAS)

AF:

0.000195

AC:

AN:

5136

South Asian (SAS)

AF:

0.0101

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0711

AC:

754

AN:

10602

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0379

AC:

2573

AN:

67920

Other (OTH)

AF:

0.0199

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

198

397

595

794

992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<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:

0.0313

Hom.:

Bravo

AF:

0.0201

Asia WGS

AF:

0.00492

AC:

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.7

(source)

DANN

Benign

0.76

PhyloP100

-0.28

PromoterAI

-0.033

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.6

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over