dbSNP rs4712026: GSTA9P:n.52946095A>G (chr6-52946095-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.149 in 152,200 control chromosomes in the GnomAD database, including 2,152 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 0.15 ( 2152 hom., cov: 32)

Consequence

GSTA9P
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.775

Publications

5 publications found

Variant links:

Genes affected

GSTA9P (HGNC:49902): (glutathione S-transferase alpha 9, pseudogene)

GSTA9P links:

ENSG00000291036 (HGNC:):

ENSG00000291036 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 (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTA9P		n.52946095A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GSTA9P	ENST00000406231.1 link	n.369-630T>C	intron_variant	Intron 4 of 5	6
ENSG00000291036	ENST00000448991.7 link	n.269-630T>C	intron_variant	Intron 3 of 5	3
ENSG00000291036	ENST00000763228.1 link	n.49-630T>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22639

AN:

152082

Hom.:

2145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.316

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.151

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

GnomAD4 genome

AF:

0.149

AC:

22677

AN:

152200

Hom.:

2152

Cov.:

AF XY:

0.156

AC XY:

11615

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.107

AC:

4445

AN:

41532

American (AMR)

AF:

0.317

AC:

4846

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

631

AN:

3472

East Asian (EAS)

AF:

0.307

AC:

1584

AN:

5166

South Asian (SAS)

AF:

0.160

AC:

775

AN:

4830

European-Finnish (FIN)

AF:

0.164

AC:

1734

AN:

10594

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8213

AN:

68012

Other (OTH)

AF:

0.152

AC:

322

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

952

1903

2855

3806

4758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.139

Hom.:

3255

Bravo

AF:

0.162

Asia WGS

AF:

0.239

AC:

830

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.2

(source)

DANN

Benign

0.65

PhyloP100

0.78

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over