22-24000111-T-A

Variant names:

• chr22-24000111-T-A
• NM_001358664.2:c.492A>T
• GSTT4 p.Ser164Ser

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001358664.2(GSTT4):​c.492A>T​(p.Ser164Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 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: -1.22
• 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP7: Synonymous conserved (PhyloP=-1.22 with no splicing effect.

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.492A>T	p.Ser164Ser	synonymous	Exon 4 of 5	NP_001345593.1	A0A1W2PR19
	GSTT4	NR_003081.3		n.438A>T		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.492A>T	p.Ser164Ser	synonymous	Exon 4 of 5	ENSP00000492273.1	A0A1W2PR19
	GSTT4	ENST00000611600.4	TSL:1	n.*134A>T		non_coding_transcript_exon	Exon 3 of 4	ENSP00000492640.1	A0A1W2PRF8
	GSTT4	ENST00000611600.4	TSL:1	n.*134A>T		3_prime_UTR	Exon 3 of 4	ENSP00000492640.1	A0A1W2PRF8

Frequencies

GnomAD3 genomes Cov.: 38

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 38

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.94
DANN	Benign	0.46
PhyloP100		-1.2

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;