GeneBe

chr19-6742853-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001288962.2(TRIP10):​c.198-114G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000803 in 1,245,110 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 30)
Exomes 𝑓: 8.0e-7 ( 0 hom. )

Consequence

TRIP10
NM_001288962.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.701
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIP10NM_001288962.2 linkc.198-114G>T intron_variant Intron 3 of 14 ENST00000313244.14 NP_001275891.1 Q15642-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIP10ENST00000313244.14 linkc.198-114G>T intron_variant Intron 3 of 14 1 NM_001288962.2 ENSP00000320117.7 Q15642-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
8.03e-7
AC:
1
AN:
1245110
Hom.:
0
AF XY:
0.00000163
AC XY:
1
AN XY:
615346
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000359
AC:
1
AN:
27860
American (AMR)
AF:
0.00
AC:
0
AN:
29062
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19422
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38142
South Asian (SAS)
AF:
0.00
AC:
0
AN:
67650
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
43730
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3468
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
963494
Other (OTH)
AF:
0.00
AC:
0
AN:
52282
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.30
DANN
Benign
0.37
PhyloP100
-0.70

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

Loading publications...

Other links and lift over

dbSNP: rs339408; hg19: chr19-6742864; API