rs7226408

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-36791898-C-A
• chr18-36791898-C-T

Variant summary

Our verdict is Likely benign. Variant got -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

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPGS2	NM_001271951.2	c.658-4819G>T		intron_variant	Intron 6 of 6		NP_001258880.1
TPGS2	NM_001330572.2	c.657+6551G>T		intron_variant	Intron 6 of 6		NP_001317501.1
TPGS2	NM_001271956.2	c.657+6551G>T		intron_variant	Intron 6 of 6		NP_001258885.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPGS2	ENST00000590842.5	c.658-4819G>T		intron_variant	Intron 6 of 6	2		ENSP00000464780.1
TPGS2	ENST00000587129.5	c.657+6551G>T		intron_variant	Intron 6 of 6	4		ENSP00000465551.1
TPGS2	ENST00000614939.4	c.657+6551G>T		intron_variant	Intron 6 of 6	4		ENSP00000478553.1

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 v4.3

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

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-34371861;