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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;