9-115059339-A-C

Position:

• chr9-115059339-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002160.4(TNC):​c.4306+391T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,966 control chromosomes in the GnomAD database, including 20,966 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 0.52 (20966 hom., cov: 32)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNC	NM_002160.4	c.4306+391T>G		intron_variant		ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9	c.4306+391T>G		intron_variant		1	NM_002160.4	ENSP00000265131	P1
DELEC1	ENST00000649121.1	n.79-24916A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78333 AN: 151848 Hom.: 20939 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.516 AC: 78407 AN: 151966 Hom.: 20966 Cov.: 32 AF XY: 0.511 AC XY: 37920 AN XY: 74244

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.458

Alfa AF: 0.472 Hom.: 7264

Bravo AF: 0.509

Asia WGS AF: 0.353 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.85

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

Other links and lift over

dbSNP: rs1060545; hg19: chr9-117821618;