XM_024452202.2:c.472-4918A>G

Variant names:

• chr22-23994133-T-C
• rs140289
• XM_024452202.2:c.472-4918A>G

Variant summary

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

The XM_024452202.2(GSTT4):​c.472-4918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 145,860 control chromosomes in the GnomAD database, including 28,763 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 0.67 (28763 hom., cov: 34)
• Consequence: GSTT4 XM_024452202.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 25 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 (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 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: 0.670 AC: 97705 AN: 145750 Hom.: 28720 Cov.: 34

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.671 AC: 97803 AN: 145860 Hom.: 28763 Cov.: 34 AF XY: 0.670 AC XY: 47698 AN XY: 71240

African (AFR) AF: 0.798 AC: 31527 AN: 39488

American (AMR) AF: 0.632 AC: 9271 AN: 14658

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2190 AN: 3332

East Asian (EAS) AF: 0.500 AC: 2511 AN: 5026

South Asian (SAS) AF: 0.655 AC: 3006 AN: 4592

European-Finnish (FIN) AF: 0.648 AC: 6529 AN: 10078

Middle Eastern (MID) AF: 0.688 AC: 194 AN: 282

European-Non Finnish (NFE) AF: 0.620 AC: 40629 AN: 65492

Other (OTH) AF: 0.671 AC: 1365 AN: 2034

Alfa AF: 0.749 Hom.: 31565

Asia WGS AF: 0.685 AC: 2384 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs140289; hg19: chr22-24336327;