Variant chr19-6751282-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001288963.3(TRIP10):c.1738T>G(p.Cys580Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,608,724 control chromosomes in the GnomAD database, including 29,568 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3871 hom., cov: 32)

Exomes 𝑓: 0.19 ( 25697 hom. )

Consequence

TRIP10
NM_001288963.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.236

Variant links:

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]

TRIP10 links:

TRIP10 (HGNC:):

TRIP10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013584793).

BP6

Variant 19-6751282-T-G is Benign according to our data. Variant chr19-6751282-T-G is described in ClinVar as [Benign]. Clinvar id is 403569.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIP10	NM_001288962.2 linkuse as main transcript	c.*71T>G		3_prime_UTR_variant	15/15	ENST00000313244.14	NP_001275891.1	Q15642-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIP10	ENST00000313244.14 linkuse as main transcript	c.*71T>G		3_prime_UTR_variant	15/15	1	NM_001288962.2	ENSP00000320117.7		Q15642-1

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33426

AN:

151888

Hom.:

3855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.204

AC:

49716

AN:

243922

Hom.:

5447

AF XY:

0.197

AC XY:

26147

AN XY:

133016

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.247

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.264

Gnomad SAS exome

AF:

0.135

Gnomad FIN exome

AF:

0.242

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.185

AC:

269531

AN:

1456718

Hom.:

25697

Cov.:

AF XY:

0.183

AC XY:

132269

AN XY:

724440

show subpopulations

Gnomad4 AFR exome

AF:

0.290

Gnomad4 AMR exome

AF:

0.245

Gnomad4 ASJ exome

AF:

0.164

Gnomad4 EAS exome

AF:

0.239

Gnomad4 SAS exome

AF:

0.135

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.220

AC:

33485

AN:

152006

Hom.:

3871

Cov.:

AF XY:

0.222

AC XY:

16467

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.152

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.191

Hom.:

4129

Bravo

AF:

0.225

TwinsUK

AF:

0.170

AC:

629

ALSPAC

AF:

0.177

AC:

683

ExAC

AF:

0.201

AC:

24325

Asia WGS

AF:

0.245

AC:

852

AN:

3478

EpiCase

AF:

0.176

EpiControl

AF:

0.188

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.62

DEOGEN2

Benign

0.0098

Eigen

Benign

-0.52

Eigen_PC

Benign

-0.48

FATHMM_MKL

Benign

0.73

LIST_S2

Benign

0.26

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.0

Vest4

0.25

ClinPred

0.00091

GERP RS

1.3

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over