Variant 9-115042265-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.5202A>G(p.Thr1734=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,613,764 control chromosomes in the GnomAD database, including 56,989 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 8182 hom., cov: 32)

Exomes 𝑓: 0.25 ( 48807 hom. )

Consequence

TNC
NM_002160.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.120

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=-0.86).

BP6

Variant 9-115042265-T-C is Benign according to our data. Variant chr9-115042265-T-C is described in ClinVar as [Benign]. Clinvar id is 1222923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 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.5202A>G	p.Thr1734=	synonymous_variant	18/28	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.5202A>G	p.Thr1734=	synonymous_variant	18/28	1	NM_002160.4	ENSP00000265131	P1	P24821-1
DELEC1	ENST00000649121.1 linkuse as main transcript	n.79-41990T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46907

AN:

152016

Hom.:

8172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.267

GnomAD3 exomes

AF:

0.242

AC:

60843

AN:

251276

Hom.:

8391

AF XY:

0.233

AC XY:

31635

AN XY:

135818

show subpopulations

Gnomad AFR exome

AF:

0.491

Gnomad AMR exome

AF:

0.241

Gnomad ASJ exome

AF:

0.202

Gnomad EAS exome

AF:

0.127

Gnomad SAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.251

AC:

367515

AN:

1461630

Hom.:

48807

Cov.:

AF XY:

0.246

AC XY:

178947

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.483

Gnomad4 AMR exome

AF:

0.247

Gnomad4 ASJ exome

AF:

0.199

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.296

Gnomad4 NFE exome

AF:

0.260

Gnomad4 OTH exome

AF:

0.247

GnomAD4 genome

AF:

0.309

AC:

46963

AN:

152134

Hom.:

8182

Cov.:

AF XY:

0.303

AC XY:

22513

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.478

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.280

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.257

Hom.:

6974

Bravo

AF:

0.315

Asia WGS

AF:

0.137

AC:

479

AN:

3478

EpiCase

AF:

0.250

EpiControl

AF:

0.249

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

-0.86

CADD

Benign

0.76

DANN

Benign

0.36

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