19-6751268-AG-GT

Variant names:

• chr19-6751268-AG-GT
• ENST00000596758.5:c.1724_1725delAGinsGT
• TRIP10 p.Glu575Gly

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001288963.3(TRIP10):​c.1724_1725delAGinsGT​(p.Glu575Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TRIP10 NM_001288963.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50
• Publications: 0 publications found

Genes affected

TRIP10 (HGNC:12304): (thyroid hormone receptor interactor 10) Enables identical protein binding activity. Predicted to be involved in actin cytoskeleton organization; endocytosis; and signal transduction. Located in nucleoplasm. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000269680 (HGNC:58603):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001288963.3. 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
	TRIP10	NM_001288962.2	MANE Select	c.*57_*58delAGinsGT		3_prime_UTR	Exon 15 of 15	NP_001275891.1	Q15642-1
	TRIP10	NM_001288963.3		c.1724_1725delAGinsGT	p.Glu575Gly	missense	N/A	NP_001275892.1	W4VSQ9
	TRIP10	NM_004240.4		c.*57_*58delAGinsGT		3_prime_UTR	Exon 14 of 14	NP_004231.1	Q15642-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIP10	ENST00000596758.5	TSL:1	c.1724_1725delAGinsGT	p.Glu575Gly	missense	N/A	ENSP00000469360.1	W4VSQ9
	TRIP10	ENST00000313244.14	TSL:1 MANE Select	c.*57_*58delAGinsGT		3_prime_UTR	Exon 15 of 15	ENSP00000320117.7	Q15642-1
	TRIP10	ENST00000313285.12	TSL:1	c.*57_*58delAGinsGT		3_prime_UTR	Exon 14 of 14	ENSP00000320493.6	Q15642-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.5

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.

Other links and lift over

hg19: chr19-6751279;