Variant 15-64393898-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_016213.5(TRIP4):c.102-47del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,488,212 control chromosomes in the GnomAD database, including 106 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0081 ( 9 hom., cov: 31)

Exomes 𝑓: 0.011 ( 97 hom. )

Consequence

TRIP4
NM_016213.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.10

Variant links:

Genes affected

TRIP4 (HGNC:12310): (thyroid hormone receptor interactor 4) This gene encodes a subunit of the tetrameric nuclear activating signal cointegrator 1 (ASC-1) complex, which associates with transcriptional coactivators, nuclear receptors and basal transcription factors to facilitate nuclear receptors-mediated transcription. This protein is localized in the nucleus and contains an E1A-type zinc finger domain, which mediates interaction with transcriptional coactivators and ligand-bound nuclear receptors, such as thyroid hormone receptor and retinoid X receptor alpha, but not glucocorticoid receptor. Mutations in this gene are associated with spinal muscular atrophy with congenital bone fractures-1 (SMABF1). [provided by RefSeq, Apr 2016]

TRIP4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-64393898-CA-C is Benign according to our data. Variant chr15-64393898-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1177845.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00807 (1228/152236) while in subpopulation NFE AF= 0.0126 (860/68024). AF 95% confidence interval is 0.0119. There are 9 homozygotes in gnomad4. There are 549 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
TRIP4	NM_016213.5 linkuse as main transcript	c.102-47del	intron_variant	ENST00000261884.8	NP_057297.2
TRIP4	NM_001321924.2 linkuse as main transcript	c.-589-47del	intron_variant		NP_001308853.1
TRIP4	NR_135855.2 linkuse as main transcript	n.130-47del	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIP4	ENST00000261884.8 linkuse as main transcript	c.102-47del		intron_variant		1	NM_016213.5	ENSP00000261884	P1

Frequencies

GnomAD3 genomes

AF:

0.00807

AC:

1228

AN:

152118

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00253

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.00833

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00349

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0126

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.00836

AC:

1480

AN:

177116

Hom.:

AF XY:

0.00834

AC XY:

796

AN XY:

95500

show subpopulations

Gnomad AFR exome

AF:

0.00239

Gnomad AMR exome

AF:

0.00626

Gnomad ASJ exome

AF:

0.00979

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00311

Gnomad FIN exome

AF:

0.00435

Gnomad NFE exome

AF:

0.0129

Gnomad OTH exome

AF:

0.00687

GnomAD4 exome

AF:

0.0105

AC:

14084

AN:

1335976

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

6884

AN XY:

658620

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.00714

Gnomad4 ASJ exome

AF:

0.00888

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00333

Gnomad4 FIN exome

AF:

0.00439

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.00920

GnomAD4 genome

AF:

0.00807

AC:

1228

AN:

152236

Hom.:

Cov.:

AF XY:

0.00737

AC XY:

549

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00253

Gnomad4 AMR

AF:

0.00832

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00349

Gnomad4 NFE

AF:

0.0126

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.00571

Hom.:

Bravo

AF:

0.00827

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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