Genetic Variant GSTA5:c.546+81G>A (chr6-52832778-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 NM_153699.3(GSTA5):c.546+81G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,598,840 control chromosomes in the GnomAD database, including 193,971 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 0.41 ( 14944 hom., cov: 31)

Exomes 𝑓: 0.49 ( 179027 hom. )

Consequence

GSTA5
NM_153699.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

Publications

7 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:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153699.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA5	NM_153699.3	MANE Select	c.546+81G>A		intron	N/A	NP_714543.1	Q7RTV2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA5	ENST00000370989.7	TSL:1 MANE Select	c.546+81G>A		intron	N/A	ENSP00000360028.1	Q7RTV2
	GSTA5	ENST00000475052.2	TSL:5	n.*248+81G>A		intron	N/A	ENSP00000518828.1	A0AAA9YHN5

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61843

AN:

151862

Hom.:

14937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.556

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.703

Gnomad SAS

AF:

0.567

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.413

GnomAD4 exome

AF:

0.491

AC:

709994

AN:

1446860

Hom.:

179027

AF XY:

0.493

AC XY:

354849

AN XY:

720310

show subpopulations

African (AFR)

AF:

0.128

AC:

4242

AN:

33184

American (AMR)

AF:

0.661

AC:

29420

AN:

44514

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

9955

AN:

25874

East Asian (EAS)

AF:

0.703

AC:

27644

AN:

39344

South Asian (SAS)

AF:

0.569

AC:

48748

AN:

85642

European-Finnish (FIN)

AF:

0.506

AC:

26743

AN:

52822

Middle Eastern (MID)

AF:

0.385

AC:

2184

AN:

5680

European-Non Finnish (NFE)

AF:

0.484

AC:

532360

AN:

1100096

Other (OTH)

AF:

0.481

AC:

28698

AN:

59704

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

17508

35016

52524

70032

87540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15724

31448

47172

62896

78620

<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:

0.407

AC:

61871

AN:

151980

Hom.:

14944

Cov.:

AF XY:

0.416

AC XY:

30892

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.149

AC:

6192

AN:

41478

American (AMR)

AF:

0.556

AC:

8497

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1379

AN:

3468

East Asian (EAS)

AF:

0.703

AC:

3619

AN:

5150

South Asian (SAS)

AF:

0.566

AC:

2721

AN:

4804

European-Finnish (FIN)

AF:

0.503

AC:

5309

AN:

10556

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.481

AC:

32661

AN:

67952

Other (OTH)

AF:

0.418

AC:

880

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1641

3282

4923

6564

8205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.453

Hom.:

6311

Bravo

AF:

0.399

Asia WGS

AF:

0.614

AC:

2135

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.3

(source)

DANN

Benign

0.63

PhyloP100

0.016

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over