rs2719

Variant names:

• chr22-23983759-G-T
• rs2719
• ENST00000634759.1:c.*153G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000634759.1(GSTT2):​c.*153G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00016 (6 hom.)
  • Failed GnomAD Quality Control
• Consequence: GSTT2 ENST00000634759.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 13 publications found

Genes affected

GSTT2 (HGNC:4642): (glutathione S-transferase theta 2 (gene/pseudogene)) The protein encoded by this gene, glutathione S-transferase (GST) theta 2 (GSTT2), is a member of a superfamily of proteins that catalyze the conjugation of reduced glutathione to a variety of electrophilic and hydrophobic compounds. Human GSTs can be divided into five main classes: alpha, mu, pi, theta, and zeta. The theta class includes GSTT1, GSTT2, and GSTT2B. GSTT2 and GSTT2B are nearly identical to each other, and share 55% amino acid identity with GSTT1. All three genes may play a role in human carcinogenesis. The GSTT2 gene is a pseudogene in some populations. [provided by RefSeq, Sep 2015]

GSTT3P (HGNC:55078): (glutathione S-transferase theta 3, pseudogene)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTT2	NR_126445.2	n.952G>T		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTT2	ENST00000634759.1	c.*153G>T		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000488993.1
GSTT3P	ENST00000437021.2	n.326+3560C>A		intron_variant	Intron 3 of 4	6
GSTT2	ENST00000402588.6	c.*153G>T		downstream_gene_variant		1		ENSP00000385765.6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 1108 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000160 AC: 16 AN: 99884 Hom.: 6 Cov.: 0 AF XY: 0.000171 AC XY: 9 AN XY: 52638

African (AFR) AF: 0.00 AC: 0 AN: 536

American (AMR) AF: 0.00 AC: 0 AN: 2618

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3230

East Asian (EAS) AF: 0.0000868 AC: 1 AN: 11524

South Asian (SAS) AF: 0.00105 AC: 11 AN: 10524

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5562

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 406

European-Non Finnish (NFE) AF: 0.0000667 AC: 4 AN: 59942

Other (OTH) AF: 0.00 AC: 0 AN: 5542

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1116 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 496

African (AFR) AF: 0.00 AC: 0 AN: 32

American (AMR) AF: 0.00 AC: 0 AN: 102

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 40

East Asian (EAS) AF: 0.00 AC: 0 AN: 166

South Asian (SAS) AF: 0.00 AC: 0 AN: 22

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 168

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 566

Other (OTH) AF: 0.00 AC: 0 AN: 12

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		0.055
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2719; hg19: chr22-24325950;