Variant 19-6751270-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000596758.5(TRIP10):c.1726C>T(p.Pro576Ser) 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 1,611,074 control chromosomes in the GnomAD database, including 29,470 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 ( 3795 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25675 hom. )

Consequence

TRIP10
ENST00000596758.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.70

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015844703).

BP6

Variant 19-6751270-C-T is Benign according to our data. Variant chr19-6751270-C-T is described in ClinVar as [Benign]. Clinvar id is 403568.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIP10	NM_001288962.2 linkuse as main transcript	c.*59C>T		3_prime_UTR_variant	15/15	ENST00000313244.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIP10	ENST00000313244.14 linkuse as main transcript	c.*59C>T		3_prime_UTR_variant	15/15	1	NM_001288962.2	P3	Q15642-1
	ENST00000594056.1 linkuse as main transcript	n.107+91G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33240

AN:

151718

Hom.:

3779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.205

GnomAD3 exomes

AF:

0.203

AC:

50086

AN:

246766

Hom.:

5427

AF XY:

0.196

AC XY:

26290

AN XY:

134250

show subpopulations

Gnomad AFR exome

AF:

0.283

Gnomad AMR exome

AF:

0.246

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.263

Gnomad SAS exome

AF:

0.134

Gnomad FIN exome

AF:

0.242

Gnomad NFE exome

AF:

0.183

Gnomad OTH exome

AF:

0.207

GnomAD4 exome

AF:

0.185

AC:

269661

AN:

1459238

Hom.:

25675

Cov.:

AF XY:

0.182

AC XY:

132321

AN XY:

725900

show subpopulations

Gnomad4 AFR exome

AF:

0.289

Gnomad4 AMR exome

AF:

0.244

Gnomad4 ASJ exome

AF:

0.165

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:

0.197

GnomAD4 genome

AF:

0.219

AC:

33299

AN:

151836

Hom.:

3795

Cov.:

AF XY:

0.221

AC XY:

16368

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.152

Gnomad4 EAS

AF:

0.274

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.210

Alfa

AF:

0.193

Hom.:

1568

Bravo

AF:

0.225

TwinsUK

AF:

0.169

AC:

627

ALSPAC

AF:

0.177

AC:

682

ExAC

AF:

0.201

AC:

24326

Asia WGS

AF:

0.245

AC:

850

AN:

3478

EpiCase

AF:

0.176

EpiControl

AF:

0.187

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

Cadd

Benign

Dann

Benign

0.77

DEOGEN2

Benign

0.0053

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.62

FATHMM_MKL

Benign

0.65

LIST_S2

Benign

0.37

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.98

MutationTaster

Benign

0.00011

P;P

Vest4

0.37

ClinPred

0.00044

GERP RS

-0.062

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