18-36791898-C-A

Variant names:

• chr18-36791898-C-A
• rs7226408
• NM_001271951.2:c.658-4819G>T

Variant summary

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

The NM_001271951.2(TPGS2):​c.658-4819G>T variant causes a intron 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: 31)
• Consequence: TPGS2 NM_001271951.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 0 publications found

Genes affected

TPGS2 (HGNC:24561): (tubulin polyglutamylase complex subunit 2) This gene encodes a protein that is a component of the neuronal polyglutamylase complex, which plays a role in post-translational addition of glutamate residues to C-terminal tubulin tails. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2012]

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=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271951.2. 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
	TPGS2	NM_001271951.2		c.658-4819G>T		intron	N/A	NP_001258880.1	Q68CL5-5
	TPGS2	NM_001330572.2		c.657+6551G>T		intron	N/A	NP_001317501.1	K7EKC0
	TPGS2	NM_001271956.2		c.657+6551G>T		intron	N/A	NP_001258885.1	A0A087WUC8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPGS2	ENST00000590842.5	TSL:2	c.658-4819G>T		intron	N/A	ENSP00000464780.1	Q68CL5-5
	TPGS2	ENST00000587129.5	TSL:4	c.657+6551G>T		intron	N/A	ENSP00000465551.1	K7EKC0
	TPGS2	ENST00000614939.4	TSL:4	c.657+6551G>T		intron	N/A	ENSP00000478553.1	A0A087WUC8

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.45
DANN	Benign	0.15
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7226408; hg19: chr18-34371861;