rs4715354

Variant names:

• chr6-52843999-G-A
• rs4715354
• XM_054328422.1:c.-31+2057C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-52843999-G-A
• chr6-52843999-G-C

Variant summary

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

The XM_054328422.1(GSTA5):​c.-31+2057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 146,544 control chromosomes in the GnomAD database, including 14,975 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 0.42 (14975 hom., cov: 32)
• Consequence: GSTA5 XM_054328422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 24 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTA5	XM_054328422.1	c.-31+2057C>T		intron_variant	Intron 1 of 6		XP_054184397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.424 AC: 62075 AN: 146428 Hom.: 14967 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.424 AC: 62107 AN: 146544 Hom.: 14975 Cov.: 32 AF XY: 0.434 AC XY: 31010 AN XY: 71468

African (AFR) AF: 0.168 AC: 6391 AN: 38098

American (AMR) AF: 0.575 AC: 8509 AN: 14786

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1382 AN: 3424

East Asian (EAS) AF: 0.714 AC: 3635 AN: 5094

South Asian (SAS) AF: 0.587 AC: 2709 AN: 4618

European-Finnish (FIN) AF: 0.520 AC: 5319 AN: 10236

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 32655 AN: 67068

Other (OTH) AF: 0.439 AC: 888 AN: 2024

Alfa AF: 0.457 Hom.: 46014

Bravo AF: 0.401

Asia WGS AF: 0.609 AC: 2116 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4715354; hg19: chr6-52708797;