Variant chr9-115024229-G-A 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 NM_002160.4(TNC):c.6332-93C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 1,382,088 control chromosomes in the GnomAD database, including 1,646 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.058 ( 321 hom., cov: 32)

Exomes 𝑓: 0.042 ( 1325 hom. )

Consequence

TNC
NM_002160.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.320

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 9-115024229-G-A is Benign according to our data. Variant chr9-115024229-G-A is described in ClinVar as [Benign]. Clinvar id is 1288564.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNC	NM_002160.4 linkuse as main transcript	c.6332-93C>T		intron_variant		ENST00000350763.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNC	ENST00000350763.9 linkuse as main transcript	c.6332-93C>T		intron_variant		1	NM_002160.4	P1	P24821-1
DELEC1	ENST00000649121.1 linkuse as main transcript	n.78+54568G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0580

AC:

8822

AN:

152142

Hom.:

320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0995

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.0529

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0110

Gnomad FIN

AF:

0.0136

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0482

Gnomad OTH

AF:

0.0527

GnomAD4 exome

AF:

0.0419

AC:

51548

AN:

1229828

Hom.:

1325

AF XY:

0.0408

AC XY:

24886

AN XY:

610400

show subpopulations

Gnomad4 AFR exome

AF:

0.0937

Gnomad4 AMR exome

AF:

0.0383

Gnomad4 ASJ exome

AF:

0.0547

Gnomad4 EAS exome

AF:

0.0000526

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.0158

Gnomad4 NFE exome

AF:

0.0453

Gnomad4 OTH exome

AF:

0.0459

GnomAD4 genome

AF:

0.0580

AC:

8830

AN:

152260

Hom.:

321

Cov.:

AF XY:

0.0551

AC XY:

4101

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0994

Gnomad4 AMR

AF:

0.0528

Gnomad4 ASJ

AF:

0.0510

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.0136

Gnomad4 NFE

AF:

0.0482

Gnomad4 OTH

AF:

0.0521

Alfa

AF:

0.0278

Hom.:

Bravo

AF:

0.0634

Asia WGS

AF:

0.0100

AC:

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 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.8

DANN

Benign

0.45

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