22-24000111-TGA-GCT

Variant names:

• chr22-24000111-TGA-GCT
• NM_001358664.2:c.490_492delTCAinsAGC
• GSTT4 p.165

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001358664.2(GSTT4):​c.490_492delTCAinsAGC​(p.165) variant causes a synonymous change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S164S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 38)
• Consequence: GSTT4 NM_001358664.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.40
• Publications: 0 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: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001358664.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTT4	NM_001358664.2	MANE Select	c.490_492delTCAinsAGC	p.165	synonymous	N/A	NP_001345593.1	A0A1W2PR19
	GSTT4	NR_003081.3		n.436_438delTCAinsAGC		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTT4	ENST00000621179.6	TSL:5 MANE Select	c.490_492delTCAinsAGC	p.165	synonymous	N/A	ENSP00000492273.1	A0A1W2PR19
	GSTT4	ENST00000611600.4	TSL:1	n.*132_*134delTCAinsAGC		non_coding_transcript_exon	Exon 3 of 4	ENSP00000492640.1	A0A1W2PRF8
	GSTT4	ENST00000611600.4	TSL:1	n.*132_*134delTCAinsAGC		3_prime_UTR	Exon 3 of 4	ENSP00000492640.1	A0A1W2PRF8

Frequencies

GnomAD3 genomes Cov.: 38

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

GnomAD4 genome Cov.: 38

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr22-24342305;