rs1049230

Variant names:

• chr19-6751270-C-G
• rs1049230
• ENST00000596758.5:c.1726C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-6751270-C-G
• chr19-6751270-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001288963.3(TRIP10):​c.1726C>G​(p.Pro576Ala) variant causes a missense 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. 12/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P576S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TRIP10 NM_001288963.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 32 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.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21862271).

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.*59C>G		3_prime_UTR	Exon 15 of 15	NP_001275891.1	Q15642-1
	TRIP10	NM_001288963.3		c.1726C>G	p.Pro576Ala	missense	Exon 14 of 14	NP_001275892.1	W4VSQ9
	TRIP10	NM_004240.4		c.*59C>G		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.1726C>G	p.Pro576Ala	missense	Exon 14 of 14	ENSP00000469360.1	W4VSQ9
	TRIP10	ENST00000313244.14	TSL:1 MANE Select	c.*59C>G		3_prime_UTR	Exon 15 of 15	ENSP00000320117.7	Q15642-1
	TRIP10	ENST00000313285.12	TSL:1	c.*59C>G		3_prime_UTR	Exon 14 of 14	ENSP00000320493.6	Q15642-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1731

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.061	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	14
DANN	Benign	0.67
DEOGEN2	Benign	0.0053	T
Eigen	Benign	-0.66
Eigen_PC	Benign	-0.62
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Benign	0.35	T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.22	T
MetaSVM	Benign	-1.0	T
PhyloP100		1.7
Vest4		0.36
MVP		0.32
ClinPred		0.047	T
GERP RS		-0.062
Mutation Taster		=98/2	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: rs1049230; hg19: chr19-6751281;