dbSNP rs13181961: TRIP13:c.92+151C>G (chr5-893241-C-G) – ACMG Classification: Benign (-20 pts)

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

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]

TRIP13 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 (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	Effect	Exon rank	MANE	Protein	UniProt
TRIP13	NM_004237.4 link	c.92+151C>G	intron_variant	Intron 1 of 12	ENST00000166345.8	NP_004228.1	Q15645-1
TRIP13	NM_001166260.2 link	c.92+151C>G	intron_variant	Intron 1 of 8		NP_001159732.1
TRIP13	XM_011514163.2 link	c.92+151C>G	intron_variant	Intron 1 of 13		XP_011512465.1	Q15645-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TRIP13	ENST00000166345.8 link	c.92+151C>G	intron_variant	Intron 1 of 12	1	NM_004237.4	ENSP00000166345.3	Q15645-1
TRIP13	ENST00000512024.5 link	n.207+151C>G	intron_variant	Intron 1 of 8	1
TRIP13	ENST00000508456.1 link	n.66+151C>G	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25089

AN:

151516

Hom.:

2190

Cov.:

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.:

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

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