chr6-52838968-T-C

Variant names:

• chr6-52838968-T-C
• rs4715353
• ENST00000370989.7:c.88-1359A>G

Variant summary

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

The ENST00000370989.7(GSTA5):​c.88-1359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,040 control chromosomes in the GnomAD database, including 29,122 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 0.61 (29122 hom., cov: 32)
• Consequence: GSTA5 ENST00000370989.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTA5	NM_153699.3	c.88-1359A>G		intron_variant	Intron 1 of 5		NP_714543.1
GSTA5	XM_054328422.1	c.88-1359A>G		intron_variant	Intron 2 of 6		XP_054184397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTA5	ENST00000370989.7	c.88-1359A>G		intron_variant	Intron 1 of 5	1		ENSP00000360028.1
GSTA5	ENST00000475052.2	n.88-1359A>G		intron_variant	Intron 1 of 4	5		ENSP00000518828.1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93211 AN: 151922 Hom.: 29104 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.613 AC: 93274 AN: 152040 Hom.: 29122 Cov.: 32 AF XY: 0.617 AC XY: 45862 AN XY: 74316

African (AFR) AF: 0.626 AC: 25938 AN: 41458

American (AMR) AF: 0.693 AC: 10598 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1980 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4525 AN: 5180

South Asian (SAS) AF: 0.659 AC: 3173 AN: 4816

European-Finnish (FIN) AF: 0.564 AC: 5949 AN: 10548

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39026 AN: 67964

Other (OTH) AF: 0.617 AC: 1305 AN: 2116

Alfa AF: 0.618 Hom.: 4605

Bravo AF: 0.624

Asia WGS AF: 0.736 AC: 2561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.14
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: rs4715353; hg19: chr6-52703766;