XM_024452202.2:c.472-3540G>T

Variant names:

• chr22-23992755-C-A
• rs5760147
• XM_024452202.2:c.472-3540G>T

Variant summary

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

The XM_024452202.2(GSTT4):​c.472-3540G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 144,176 control chromosomes in the GnomAD database, including 16,062 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 0.50 (16062 hom., cov: 28)
• Consequence: GSTT4 XM_024452202.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 13 publications found

Genes affected

GSTT4 (HGNC:26930): (glutathione S-transferase theta 4) Predicted to enable glutathione transferase activity. Predicted to be involved in glutathione metabolic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=6.259).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTT4	XM_024452202.2	c.472-3540G>T		intron_variant	Intron 3 of 3		XP_024307970.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.496 AC: 71519 AN: 144058 Hom.: 16059 Cov.: 28

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.496 AC: 71540 AN: 144176 Hom.: 16062 Cov.: 28 AF XY: 0.503 AC XY: 35315 AN XY: 70234

African (AFR) AF: 0.330 AC: 12953 AN: 39202

American (AMR) AF: 0.571 AC: 8173 AN: 14320

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1743 AN: 3336

East Asian (EAS) AF: 0.367 AC: 1815 AN: 4940

South Asian (SAS) AF: 0.608 AC: 2709 AN: 4458

European-Finnish (FIN) AF: 0.579 AC: 5723 AN: 9882

Middle Eastern (MID) AF: 0.571 AC: 160 AN: 280

European-Non Finnish (NFE) AF: 0.565 AC: 36644 AN: 64896

Other (OTH) AF: 0.511 AC: 1030 AN: 2014

Alfa AF: 0.524 Hom.: 5106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	6.3
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs5760147; hg19: -;