rs1547692

Variant names:

• chr9-115050066-A-G
• rs1547692
• NM_002160.4:c.4580-1534T>C

Variant summary

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

The NM_002160.4(TNC):​c.4580-1534T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,930 control chromosomes in the GnomAD database, including 30,412 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 0.63 (30412 hom., cov: 31)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNC	NM_002160.4	c.4580-1534T>C		intron_variant	Intron 15 of 27	ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9	c.4580-1534T>C		intron_variant	Intron 15 of 27	1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95287 AN: 151812 Hom.: 30380 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.628 AC: 95364 AN: 151930 Hom.: 30412 Cov.: 31 AF XY: 0.626 AC XY: 46448 AN XY: 74244

African (AFR) AF: 0.730 AC: 30249 AN: 41452

American (AMR) AF: 0.530 AC: 8083 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2406 AN: 5156

South Asian (SAS) AF: 0.490 AC: 2360 AN: 4814

European-Finnish (FIN) AF: 0.673 AC: 7089 AN: 10528

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41369 AN: 67940

Other (OTH) AF: 0.593 AC: 1253 AN: 2114

Alfa AF: 0.631 Hom.: 3988

Bravo AF: 0.621

Asia WGS AF: 0.484 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.23
PhyloP100		0.14
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: rs1547692; hg19: chr9-117812345;