dbSNP rs3789873: TNC:c.3214+668G>C (chr9-115072935-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002160.4(TNC):c.3214+668G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 151,854 control chromosomes in the GnomAD database, including 43,338 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 43338 hom., cov: 32)

Consequence

TNC
NM_002160.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0210

Publications

6 publications found

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:

LOC124902256 (HGNC:):

LOC124902256 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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002160.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TNC	NM_002160.4	MANE Select	c.3214+668G>C	intron	N/A	NP_002151.2	P24821-1
TNC	NM_001439065.1		c.3214+668G>C	intron	N/A	NP_001425994.1
TNC	NM_001439066.1		c.3214+668G>C	intron	N/A	NP_001425995.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TNC	ENST00000350763.9	TSL:1 MANE Select	c.3214+668G>C	intron	N/A	ENSP00000265131.4	P24821-1
TNC	ENST00000423613.6	TSL:1	c.3214+668G>C	intron	N/A	ENSP00000411406.2	E9PC84
TNC	ENST00000542877.6	TSL:1	c.3214+668G>C	intron	N/A	ENSP00000442242.1	F5H7V9

Frequencies

GnomAD3 genomes

AF:

0.750

AC:

113776

AN:

151734

Hom.:

43279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.853

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.652

Gnomad ASJ

AF:

0.734

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.762

Gnomad MID

AF:

0.841

Gnomad NFE

AF:

0.739

Gnomad OTH

AF:

0.745

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.750

AC:

113888

AN:

151854

Hom.:

43338

Cov.:

AF XY:

0.746

AC XY:

55319

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.853

AC:

35369

AN:

41452

American (AMR)

AF:

0.652

AC:

9947

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.734

AC:

2547

AN:

3468

East Asian (EAS)

AF:

0.447

AC:

2302

AN:

5150

South Asian (SAS)

AF:

0.609

AC:

2931

AN:

4812

European-Finnish (FIN)

AF:

0.762

AC:

8020

AN:

10524

Middle Eastern (MID)

AF:

0.856

AC:

250

AN:

292

European-Non Finnish (NFE)

AF:

0.739

AC:

50186

AN:

67882

Other (OTH)

AF:

0.746

AC:

1570

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1435

2869

4304

5738

7173

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

838

1676

2514

3352

4190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.757

Hom.:

5450

Bravo

AF:

0.745

Asia WGS

AF:

0.574

AC:

2002

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.0

(source)

DANN

Benign

0.37

PhyloP100

-0.021

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over