rs5760147

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-23992755-C-A
• chr22-23992755-C-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.

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: 0.496 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 v4.9

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;