Variant chr9-115042388-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000350763.9(TNC):c.5126-47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,604,146 control chromosomes in the GnomAD database, including 15,622 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1039 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14583 hom. )

Consequence

TNC
ENST00000350763.9 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0510

Variant links:

Genes affected

TNC (HGNC:5318): (tenascin C) This gene encodes an extracellular matrix protein with a spatially and temporally restricted tissue distribution. This protein is homohexameric with disulfide-linked subunits, and contains multiple EGF-like and fibronectin type-III domains. It is implicated in guidance of migrating neurons as well as axons during development, synaptic plasticity, and neuronal regeneration. [provided by RefSeq, Jul 2011]

TNC links:

DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]

DELEC1 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=-0.8).

BP6

Variant 9-115042388-T-C is Benign according to our data. Variant chr9-115042388-T-C is described in ClinVar as [Benign]. Clinvar id is 1274158.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNC	NM_002160.4 linkuse as main transcript	c.5126-47A>G		intron_variant		ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9 linkuse as main transcript	c.5126-47A>G		intron_variant		1	NM_002160.4	ENSP00000265131	P1	P24821-1
DELEC1	ENST00000649121.1 linkuse as main transcript	n.79-41867T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0996

AC:

15155

AN:

152186

Hom.:

1038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0245

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.0727

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.0875

GnomAD3 exomes

AF:

0.108

AC:

26324

AN:

244230

Hom.:

1877

AF XY:

0.112

AC XY:

14835

AN XY:

132244

show subpopulations

Gnomad AFR exome

AF:

0.0243

Gnomad AMR exome

AF:

0.0456

Gnomad ASJ exome

AF:

0.0516

Gnomad EAS exome

AF:

0.000222

Gnomad SAS exome

AF:

0.122

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.148

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.135

AC:

196252

AN:

1451842

Hom.:

14583

Cov.:

AF XY:

0.135

AC XY:

97811

AN XY:

721992

show subpopulations

Gnomad4 AFR exome

AF:

0.0197

Gnomad4 AMR exome

AF:

0.0466

Gnomad4 ASJ exome

AF:

0.0534

Gnomad4 EAS exome

AF:

0.000303

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.150

Gnomad4 OTH exome

AF:

0.116

GnomAD4 genome

AF:

0.0995

AC:

15156

AN:

152304

Hom.:

1039

Cov.:

AF XY:

0.0983

AC XY:

7324

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0244

Gnomad4 AMR

AF:

0.0727

Gnomad4 ASJ

AF:

0.0625

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.110

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.0866

Alfa

AF:

0.128

Hom.:

347

Bravo

AF:

0.0882

Asia WGS

AF:

0.0480

AC:

166

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.1

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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