Variant 5-893106-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2

The ENST00000166345.8(TRIP13):c.92+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0096 in 1,575,356 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0099 ( 107 hom. )

Consequence

TRIP13
ENST00000166345.8 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.00

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 5-893106-C-T is Benign according to our data. Variant chr5-893106-C-T is described in ClinVar as [Benign]. Clinvar id is 2801949.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00632 (962/152210) while in subpopulation SAS AF= 0.0112 (54/4824). AF 95% confidence interval is 0.00959. There are 3 homozygotes in gnomad4. There are 454 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TRIP13	NM_004237.4 linkuse as main transcript	c.92+16C>T	intron_variant	ENST00000166345.8	NP_004228.1	Q15645-1
TRIP13	NM_001166260.2 linkuse as main transcript	c.92+16C>T	intron_variant		NP_001159732.1
TRIP13	XM_011514163.2 linkuse as main transcript	c.92+16C>T	intron_variant		XP_011512465.1	Q15645-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
TRIP13	ENST00000166345.8 linkuse as main transcript	c.92+16C>T	intron_variant	1	NM_004237.4	ENSP00000166345.3	Q15645-1
TRIP13	ENST00000512024.5 linkuse as main transcript	n.207+16C>T	intron_variant	1
TRIP13	ENST00000508456.1 linkuse as main transcript	n.66+16C>T	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.00633

AC:

962

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00196

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00183

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00834

AC:

1527

AN:

183102

Hom.:

AF XY:

0.00889

AC XY:

892

AN XY:

100294

show subpopulations

Gnomad AFR exome

AF:

0.00185

Gnomad AMR exome

AF:

0.00238

Gnomad ASJ exome

AF:

0.0120

Gnomad EAS exome

AF:

0.0000680

Gnomad SAS exome

AF:

0.0136

Gnomad FIN exome

AF:

0.00555

Gnomad NFE exome

AF:

0.0112

Gnomad OTH exome

AF:

0.00634

GnomAD4 exome

AF:

0.00995

AC:

14158

AN:

1423146

Hom.:

107

Cov.:

AF XY:

0.0100

AC XY:

7064

AN XY:

705772

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00247

Gnomad4 ASJ exome

AF:

0.0122

Gnomad4 EAS exome

AF:

0.0000260

Gnomad4 SAS exome

AF:

0.0133

Gnomad4 FIN exome

AF:

0.00567

Gnomad4 NFE exome

AF:

0.0107

Gnomad4 OTH exome

AF:

0.00935

GnomAD4 genome

AF:

0.00632

AC:

962

AN:

152210

Hom.:

Cov.:

AF XY:

0.00610

AC XY:

454

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00183

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0112

Gnomad4 FIN

AF:

0.00480

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00433

Hom.:

Bravo

AF:

0.00567

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

6.7

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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