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rs12347433

chr9-115035318-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_002160.4(TNC):c.5673A>G(p.Arg1891=) 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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=3.05 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
TNCNM_002160.4 linkuse as main transcriptc.5673A>G p.Arg1891= synonymous_variant 22/28 ENST00000350763.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TNCENST00000350763.9 linkuse as main transcriptc.5673A>G p.Arg1891= synonymous_variant 22/281 NM_002160.4 P1P24821-1
DELEC1ENST00000649121.1 linkuse as main transcriptn.79-48937T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.205
AC:
31214
AN:
152000
Hom.:
3657
Cov.:
32
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.:
33
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.205
AC:
31212
AN:
152118
Hom.:
3656
Cov.:
32
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:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxDec 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
12
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.

Other links and lift over

dbSNP: rs12347433; hg19: chr9-117797597; COSMIC: COSV60780714; COSMIC: COSV60780714; API