rs140289

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-23994133-T-C
• chr22-23994133-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTT4	XM_024452202.2	c.472-4918A>G		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: 0.670 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 v4.3

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;