22-26524082-T-G

Variant names:

• chr22-26524082-T-G
• rs3088103
• NM_003595.5:c.*2193A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003595.5(TPST2):​c.*2193A>C variant causes a 3 prime UTR 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TPST2 NM_003595.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 9 publications found

Genes affected

TPST2 (HGNC:12021): (tyrosylprotein sulfotransferase 2) The protein encoded by this gene catalyzes the O-sulfation of tyrosine residues within acidic regions of proteins. The encoded protein is a type II integral membrane protein found in the Golgi body. Alternative splicing produces multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2018]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003595.5. 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
	TPST2	NM_003595.5	MANE Select	c.*2193A>C		3_prime_UTR	Exon 7 of 7	NP_003586.3
	TPST2	NM_001362923.2		c.*2193A>C		3_prime_UTR	Exon 8 of 8	NP_001349852.1
	TPST2	NM_001008566.3		c.*2193A>C		3_prime_UTR	Exon 7 of 7	NP_001008566.1	O60704

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPST2	ENST00000338754.9	TSL:1 MANE Select	c.*2193A>C		3_prime_UTR	Exon 7 of 7	ENSP00000339813.4	O60704
	TPST2	ENST00000454778.6	TSL:4	c.*2193A>C		splice_region	Exon 7 of 7	ENSP00000400357.2	O60704
	TPST2	ENST00000454778.6	TSL:4	c.*2193A>C		3_prime_UTR	Exon 7 of 7	ENSP00000400357.2	O60704

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		-0.15

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: rs3088103; hg19: chr22-26920048;