chr6-52838598-C-T

Position:

• chr6-52838598-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153699.3(GSTA5):​c.88-989G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,200 control chromosomes in the GnomAD database, including 2,857 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 0.16 (2857 hom., cov: 33)
• Consequence: GSTA5 NM_153699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSTA5	NM_153699.3	c.88-989G>A		intron_variant			NP_714543.1
GSTA5	XM_054328422.1	c.88-989G>A		intron_variant			XP_054184397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTA5	ENST00000370989.6	c.88-989G>A		intron_variant		1		ENSP00000360028.1
GSTA5	ENST00000475052.1	n.118-989G>A		intron_variant		5		ENSP00000518828.1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25100 AN: 152082 Hom.: 2852 Cov.: 33

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.165 AC: 25107 AN: 152200 Hom.: 2857 Cov.: 33 AF XY: 0.168 AC XY: 12514 AN XY: 74412

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.159

Alfa AF: 0.202 Hom.: 3594

Bravo AF: 0.173

Asia WGS AF: 0.171 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.52

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

LitVar

Other links and lift over

dbSNP: rs4715352; hg19: chr6-52703396;