rs13181961

Variant summary

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

The NM_004237.4(TRIP13):​c.92+151C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 785,572 control chromosomes in the GnomAD database, including 13,498 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2190 hom., cov: 30)
Exomes 𝑓: 0.18 ( 11308 hom. )

Consequence

TRIP13
NM_004237.4 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.273
Variant links:
Genes affected
TRIP13 (HGNC:12307): (thyroid hormone receptor interactor 13) This gene encodes a protein that interacts with thyroid hormone receptors, also known as hormone-dependent transcription factors. The gene product interacts specifically with the ligand binding domain. This gene is one of several that may play a role in early-stage non-small cell lung cancer. [provided by RefSeq, Oct 2009]

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 (BayesDel_noAF=-0.49).
BP6
Variant 5-893241-C-G is Benign according to our data. Variant chr5-893241-C-G is described in ClinVar as [Benign]. Clinvar id is 1235943.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIP13NM_004237.4 linkc.92+151C>G intron_variant Intron 1 of 12 ENST00000166345.8 NP_004228.1 Q15645-1
TRIP13NM_001166260.2 linkc.92+151C>G intron_variant Intron 1 of 8 NP_001159732.1
TRIP13XM_011514163.2 linkc.92+151C>G intron_variant Intron 1 of 13 XP_011512465.1 Q15645-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIP13ENST00000166345.8 linkc.92+151C>G intron_variant Intron 1 of 12 1 NM_004237.4 ENSP00000166345.3 Q15645-1
TRIP13ENST00000512024.5 linkn.207+151C>G intron_variant Intron 1 of 8 1
TRIP13ENST00000508456.1 linkn.66+151C>G intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.166
AC:
25089
AN:
151516
Hom.:
2190
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.109
Gnomad AMI
AF:
0.240
Gnomad AMR
AF:
0.154
Gnomad ASJ
AF:
0.162
Gnomad EAS
AF:
0.125
Gnomad SAS
AF:
0.156
Gnomad FIN
AF:
0.231
Gnomad MID
AF:
0.204
Gnomad NFE
AF:
0.195
Gnomad OTH
AF:
0.176
GnomAD4 exome
AF:
0.181
AC:
114665
AN:
633936
Hom.:
11308
AF XY:
0.180
AC XY:
58612
AN XY:
325184
show subpopulations
Gnomad4 AFR exome
AF:
0.105
Gnomad4 AMR exome
AF:
0.133
Gnomad4 ASJ exome
AF:
0.160
Gnomad4 EAS exome
AF:
0.131
Gnomad4 SAS exome
AF:
0.158
Gnomad4 FIN exome
AF:
0.229
Gnomad4 NFE exome
AF:
0.189
Gnomad4 OTH exome
AF:
0.177
GnomAD4 genome
AF:
0.165
AC:
25090
AN:
151636
Hom.:
2190
Cov.:
30
AF XY:
0.168
AC XY:
12482
AN XY:
74110
show subpopulations
Gnomad4 AFR
AF:
0.109
Gnomad4 AMR
AF:
0.154
Gnomad4 ASJ
AF:
0.162
Gnomad4 EAS
AF:
0.125
Gnomad4 SAS
AF:
0.155
Gnomad4 FIN
AF:
0.231
Gnomad4 NFE
AF:
0.195
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.186
Hom.:
351
Bravo
AF:
0.156
Asia WGS
AF:
0.133
AC:
463
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Jun 14, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
5.5
DANN
Benign
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs13181961; hg19: chr5-893356; API