ENST00000370989.7:c.415-459C>G

Variant names:

• chr6-52833449-G-C
• rs9370155
• NM_153699.3:c.415-459C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000370989.7(GSTA5):​c.415-459C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,102 control chromosomes in the GnomAD database, including 1,499 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 0.11 (1499 hom., cov: 32)
• Consequence: GSTA5 ENST00000370989.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 0 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370989.7. 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
	GSTA5	NM_153699.3	MANE Select	c.415-459C>G		intron	N/A	NP_714543.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTA5	ENST00000370989.7	TSL:1 MANE Select	c.415-459C>G		intron	N/A	ENSP00000360028.1
	GSTA5	ENST00000475052.2	TSL:5	n.*117-459C>G		intron	N/A	ENSP00000518828.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16630 AN: 151984 Hom.: 1492 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0682

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.109 AC: 16642 AN: 152102 Hom.: 1499 Cov.: 32 AF XY: 0.112 AC XY: 8359 AN XY: 74352

African (AFR) AF: 0.0271 AC: 1124 AN: 41494

American (AMR) AF: 0.295 AC: 4499 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0438 AC: 152 AN: 3470

East Asian (EAS) AF: 0.141 AC: 728 AN: 5166

South Asian (SAS) AF: 0.0687 AC: 331 AN: 4818

European-Finnish (FIN) AF: 0.0982 AC: 1039 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8481 AN: 67988

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.126 Hom.: 184

Bravo AF: 0.122

Asia WGS AF: 0.116 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.075
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9370155; hg19: chr6-52698247;