Variant 9-115035318-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002160.4(TNC):c.5673A>G(p.Arg1891Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,611,976 control chromosomes in the GnomAD database, including 54,366 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3656 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50710 hom. )

Consequence

TNC
NM_002160.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.05

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 9-115035318-T-C is Benign according to our data. Variant chr9-115035318-T-C is described in ClinVar as [Benign]. Clinvar id is 1182259.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNC	NM_002160.4 link	c.5673A>G	p.Arg1891Arg	synonymous_variant	22/28	ENST00000350763.9	NP_002151.2	P24821-1Q4LE33B4E1W8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9 link	c.5673A>G	p.Arg1891Arg	synonymous_variant	22/28	1	NM_002160.4	ENSP00000265131.4		P24821-1

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31214

AN:

152000

Hom.:

3657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0905

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.209

GnomAD3 exomes

AF:

0.227

AC:

56401

AN:

248602

Hom.:

7033

AF XY:

0.229

AC XY:

30784

AN XY:

134470

show subpopulations

Gnomad AFR exome

AF:

0.0858

Gnomad AMR exome

AF:

0.195

Gnomad ASJ exome

AF:

0.156

Gnomad EAS exome

AF:

0.165

Gnomad SAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.274

Gnomad NFE exome

AF:

0.280

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.258

AC:

376242

AN:

1459858

Hom.:

50710

Cov.:

AF XY:

0.255

AC XY:

185075

AN XY:

726258

show subpopulations

Gnomad4 AFR exome

AF:

0.0814

Gnomad4 AMR exome

AF:

0.192

Gnomad4 ASJ exome

AF:

0.156

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.161

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.280

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.205

AC:

31212

AN:

152118

Hom.:

3656

Cov.:

AF XY:

0.202

AC XY:

15015

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.0904

Gnomad4 AMR

AF:

0.202

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.277

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.259

Hom.:

9467

Bravo

AF:

0.198

Asia WGS

AF:

0.154

AC:

535

AN:

3478

EpiCase

AF:

0.273

EpiControl

AF:

0.272

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 06, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.79

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