Genetic Variant ENST00000370989.7:c.163G>A (chr6-52836345-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000370989.7(GSTA5):c.163G>A(p.Val55Ile) variant causes a missense change. The variant allele was found at a frequency of 0.945 in 1,613,558 control chromosomes in the GnomAD database, including 721,385 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.92 ( 65244 hom., cov: 31)

Exomes 𝑓: 0.95 ( 656141 hom. )

Consequence

GSTA5
ENST00000370989.7 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.38

Publications

30 publications found

Variant links:

Genes affected

GSTA5 (HGNC:19662): (glutathione S-transferase alpha 5) The glutathione S-transferases (GST; EC 2.5.1.18) catalyze the conjugation of reduced glutathiones and a variety of electrophiles, including many known carcinogens and mutagens. The cytosolic GSTs belong to a large superfamily, with members located on different chromosomes. For additional information on GSTs, see GSTA1 (MIM 138359).[supplied by OMIM, Sep 2008]

GSTA5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.91303E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTA5	NM_153699.3 link	c.163G>A	p.Val55Ile	missense_variant	Exon 3 of 6		NP_714543.1	Q7RTV2
GSTA5	XM_054328422.1 link	c.163G>A	p.Val55Ile	missense_variant	Exon 4 of 7		XP_054184397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTA5	ENST00000370989.7 link	c.163G>A	p.Val55Ile	missense_variant	Exon 3 of 6	1		ENSP00000360028.1		Q7RTV2
GSTA5	ENST00000475052.2 link	n.139+1213G>A		intron_variant	Intron 2 of 4	5		ENSP00000518828.1

Frequencies

GnomAD3 genomes

AF:

0.925

AC:

140643

AN:

152068

Hom.:

65217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.870

Gnomad AMI

AF:

0.995

Gnomad AMR

AF:

0.958

Gnomad ASJ

AF:

0.974

Gnomad EAS

AF:

0.877

Gnomad SAS

AF:

0.866

Gnomad FIN

AF:

0.892

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.960

Gnomad OTH

AF:

0.934

GnomAD2 exomes

AF:

0.933

AC:

234692

AN:

251420

AF XY:

0.931

show subpopulations

Gnomad AFR exome

AF:

0.864

Gnomad AMR exome

AF:

0.974

Gnomad ASJ exome

AF:

0.977

Gnomad EAS exome

AF:

0.878

Gnomad FIN exome

AF:

0.892

Gnomad NFE exome

AF:

0.961

Gnomad OTH exome

AF:

0.946

GnomAD4 exome

AF:

0.947

AC:

1384030

AN:

1461374

Hom.:

656141

Cov.:

AF XY:

0.945

AC XY:

687272

AN XY:

727046

show subpopulations

African (AFR)

AF:

0.866

AC:

28971

AN:

33456

American (AMR)

AF:

0.971

AC:

43447

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.976

AC:

25512

AN:

26128

East Asian (EAS)

AF:

0.876

AC:

34766

AN:

39692

South Asian (SAS)

AF:

0.871

AC:

75124

AN:

86218

European-Finnish (FIN)

AF:

0.892

AC:

47630

AN:

53386

Middle Eastern (MID)

AF:

0.953

AC:

5497

AN:

5768

European-Non Finnish (NFE)

AF:

0.959

AC:

1066427

AN:

1111628

Other (OTH)

AF:

0.938

AC:

56656

AN:

60376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

3425

6850

10275

13700

17125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21604

43208

64812

86416

108020

<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:

0.925

AC:

140720

AN:

152184

Hom.:

65244

Cov.:

AF XY:

0.921

AC XY:

68506

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.869

AC:

36082

AN:

41500

American (AMR)

AF:

0.958

AC:

14661

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.974

AC:

3383

AN:

3472

East Asian (EAS)

AF:

0.877

AC:

4529

AN:

5166

South Asian (SAS)

AF:

0.866

AC:

4152

AN:

4792

European-Finnish (FIN)

AF:

0.892

AC:

9460

AN:

10610

Middle Eastern (MID)

AF:

0.956

AC:

281

AN:

294

European-Non Finnish (NFE)

AF:

0.960

AC:

65292

AN:

68026

Other (OTH)

AF:

0.935

AC:

1973

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

507

1013

1520

2026

2533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.948

Hom.:

45485

Bravo

AF:

0.930

TwinsUK

AF:

0.959

AC:

3556

ALSPAC

AF:

0.958

AC:

3693

ESP6500AA

AF:

0.867

AC:

3818

ESP6500EA

AF:

0.964

AC:

8291

ExAC

AF:

0.931

AC:

112982

Asia WGS

AF:

0.856

AC:

2980

AN:

3478

EpiCase

AF:

0.963

EpiControl

AF:

0.962

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.012

T;T

Eigen

Benign

0.018

Eigen_PC

Benign

0.0050

FATHMM_MKL

Uncertain

0.88

LIST_S2

Uncertain

0.94

.;D

MetaRNN

Benign

0.0000039

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.8

M;M

PhyloP100

4.4

PrimateAI

Benign

0.39

PROVEAN

Benign

-0.83

N;N

REVEL

Benign

0.14

Sift

Benign

0.036

D;D

Sift4G

Uncertain

0.045

D;D

Polyphen

0.32

B;B

Vest4

0.086

MPC

0.023

ClinPred

0.041

GERP RS

2.6

Varity_R

0.13

gMVP

0.080

Mutation Taster

=100/0

polymorphism (auto)

(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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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