NM_002160.4:c.6496-6dupT

Variant names:

• chr9-115021272-T-TA
• rs5900112
• NM_002160.4:c.6496-6dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_002160.4(TNC):​c.6496-6dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 1,304,716 control chromosomes in the GnomAD database, including 3 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0028 (2 hom., cov: 24)
  • Exomes 𝑓: 0.013 (1 hom.)
• Consequence: TNC NM_002160.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.0131 (15173/1160304) while in subpopulation AFR AF= 0.0257 (610/23772). AF 95% confidence interval is 0.024. There are 1 homozygotes in gnomad4_exome. There are 7360 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 400 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNC	NM_002160.4	c.6496-6dupT		splice_region_variant, intron_variant	Intron 27 of 27	ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9	c.6496-6_6496-5insT		splice_region_variant, intron_variant	Intron 27 of 27	1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.00276 AC: 398 AN: 144338 Hom.: 2 Cov.: 24

Gnomad AFR AF: 0.00569

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00138

Gnomad ASJ AF: 0.000297

Gnomad EAS AF: 0.000603

Gnomad SAS AF: 0.00600

Gnomad FIN AF: 0.000542

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00174

Gnomad OTH AF: 0.00359

GnomAD4 exome AF: 0.0131 AC: 15173 AN: 1160304 Hom.: 1 Cov.: 0 AF XY: 0.0127 AC XY: 7360 AN XY: 577374

Gnomad4 AFR exome AF: 0.0257

Gnomad4 AMR exome AF: 0.0138

Gnomad4 ASJ exome AF: 0.0127

Gnomad4 EAS exome AF: 0.00926

Gnomad4 SAS exome AF: 0.0198

Gnomad4 FIN exome AF: 0.00632

Gnomad4 NFE exome AF: 0.0127

Gnomad4 OTH exome AF: 0.0133

GnomAD4 genome AF: 0.00277 AC: 400 AN: 144412 Hom.: 2 Cov.: 24 AF XY: 0.00289 AC XY: 202 AN XY: 70016

Gnomad4 AFR AF: 0.00572

Gnomad4 AMR AF: 0.00138

Gnomad4 ASJ AF: 0.000297

Gnomad4 EAS AF: 0.000605

Gnomad4 SAS AF: 0.00601

Gnomad4 FIN AF: 0.000542

Gnomad4 NFE AF: 0.00174

Gnomad4 OTH AF: 0.00356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs5900112; hg19: chr9-117783551;