NM_002160.4:c.4580-3179G>A

Variant names:

• chr9-115051711-C-T
• rs1330363
• NM_002160.4:c.4580-3179G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002160.4(TNC):​c.4580-3179G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,196 control chromosomes in the GnomAD database, including 29,235 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 0.62 (29235 hom., cov: 30)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 12 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNC	NM_002160.4	MANE Select	c.4580-3179G>A		intron	N/A	NP_002151.2
	TNC	NM_001439065.1		c.5128+1029G>A		intron	N/A	NP_001425994.1
	TNC	NM_001439066.1		c.5128+1029G>A		intron	N/A	NP_001425995.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNC	ENST00000350763.9	TSL:1 MANE Select	c.4580-3179G>A		intron	N/A	ENSP00000265131.4
	TNC	ENST00000423613.6	TSL:1	c.4306+8019G>A		intron	N/A	ENSP00000411406.2
	TNC	ENST00000542877.6	TSL:1	c.3763+1029G>A		intron	N/A	ENSP00000442242.1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93414 AN: 151080 Hom.: 29204 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.622

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.618 AC: 93488 AN: 151196 Hom.: 29235 Cov.: 30 AF XY: 0.616 AC XY: 45488 AN XY: 73846

African (AFR) AF: 0.701 AC: 28891 AN: 41186

American (AMR) AF: 0.524 AC: 7975 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1756 AN: 3462

East Asian (EAS) AF: 0.465 AC: 2395 AN: 5146

South Asian (SAS) AF: 0.488 AC: 2342 AN: 4804

European-Finnish (FIN) AF: 0.672 AC: 6989 AN: 10408

Middle Eastern (MID) AF: 0.638 AC: 185 AN: 290

European-Non Finnish (NFE) AF: 0.607 AC: 41119 AN: 67686

Other (OTH) AF: 0.587 AC: 1232 AN: 2100

Alfa AF: 0.606 Hom.: 8257

Bravo AF: 0.613

Asia WGS AF: 0.480 AC: 1675 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1330363; hg19: chr9-117813990;