Genetic Variant GSTT4:p.Ser164Ser (chr22-24000111-T-C) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_001358664.2(GSTT4):c.492A>G(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)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GSTT4
NM_001358664.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

0 publications found

Variant links:

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]

GSTT4 links:

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ACMG classification

Classification was made for transcript

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=-0.65).

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>G	p.Ser164Ser	synonymous	Exon 4 of 5	NP_001345593.1	A0A1W2PR19
	GSTT4	NR_003081.3		n.438A>G		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GSTT4	ENST00000621179.6	TSL:5 MANE Select	c.492A>G	p.Ser164Ser	synonymous	Exon 4 of 5	ENSP00000492273.1	A0A1W2PR19
GSTT4	ENST00000611600.4	TSL:1	n.*134A>G		non_coding_transcript_exon	Exon 3 of 4	ENSP00000492640.1	A0A1W2PRF8
GSTT4	ENST00000611600.4	TSL:1	n.*134A>G		3_prime_UTR	Exon 3 of 4	ENSP00000492640.1	A0A1W2PRF8

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

4336

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

2696

African (AFR)

AF:

0.00

AC:

AN:

104

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

124

European-Finnish (FIN)

AF:

0.00

AC:

AN:

544

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1640

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1558

Other (OTH)

AF:

0.00

AC:

AN:

308

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

1.1

(source)

DANN

Benign

0.38

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over