Variant 5-894996-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000166345.8(TRIP13):c.258+48delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,556,302 control chromosomes in the GnomAD database, including 37,006 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 13758 hom., cov: 26)

Exomes 𝑓: 0.14 ( 23248 hom. )

Consequence

TRIP13
ENST00000166345.8 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.00

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:

TRIP13 (HGNC:):

TRIP13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-894996-CA-C is Benign according to our data. Variant chr5-894996-CA-C is described in ClinVar as [Benign]. Clinvar id is 1225568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TRIP13	NM_004237.4 linkuse as main transcript	c.258+48delA	intron_variant	ENST00000166345.8	NP_004228.1	Q15645-1
TRIP13	NM_001166260.2 linkuse as main transcript	c.258+48delA	intron_variant		NP_001159732.1
TRIP13	XM_011514163.2 linkuse as main transcript	c.258+48delA	intron_variant		XP_011512465.1	Q15645-1
TRIP13	XM_047417879.1 linkuse as main transcript	c.-202+48delA	intron_variant		XP_047273835.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
TRIP13	ENST00000166345.8 linkuse as main transcript	c.258+48delA	intron_variant	1	NM_004237.4	ENSP00000166345.3	Q15645-1
TRIP13	ENST00000512024.5 linkuse as main transcript	n.373+48delA	intron_variant	1
TRIP13	ENST00000513435.1 linkuse as main transcript	c.243+48delA	intron_variant	5		ENSP00000427528.1	H0YAL2
TRIP13	ENST00000508456.1 linkuse as main transcript	n.232+48delA	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47638

AN:

151920

Hom.:

13697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.758

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.0984

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.200

AC:

41955

AN:

210044

Hom.:

7733

AF XY:

0.184

AC XY:

21019

AN XY:

114036

show subpopulations

Gnomad AFR exome

AF:

0.777

Gnomad AMR exome

AF:

0.270

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.348

Gnomad SAS exome

AF:

0.220

Gnomad FIN exome

AF:

0.0988

Gnomad NFE exome

AF:

0.0963

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.137

AC:

192097

AN:

1404264

Hom.:

23248

Cov.:

AF XY:

0.137

AC XY:

95051

AN XY:

695528

show subpopulations

Gnomad4 AFR exome

AF:

0.791

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.134

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.213

Gnomad4 FIN exome

AF:

0.0970

Gnomad4 NFE exome

AF:

0.0997

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.314

AC:

47766

AN:

152038

Hom.:

13758

Cov.:

AF XY:

0.312

AC XY:

23195

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.759

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.140

Gnomad4 EAS

AF:

0.347

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0984

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.195

Hom.:

1165

Bravo

AF:

0.349

Asia WGS

AF:

0.325

AC:

1131

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 26, 2019

- -

Oocyte maturation defect 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Mosaic variegated aneuploidy syndrome 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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