rs766737426

Variant names:

• chr9-115021283-AAGAGAGAG-A
• rs766737426
• NM_002160.4:c.6496-24_6496-17delCTCTCTCT

Your query was ambiguous. Multiple possible variants found:

• chr9-115021283-AAGAGAGAG-A
• chr9-115021283-AAGAGAGAG-AAG
• chr9-115021283-AAGAGAGAG-AAGAG
• chr9-115021283-AAGAGAGAG-AAGAGAG
• chr9-115021283-AAGAGAGAG-AAGAGAGAGAG
• chr9-115021283-AAGAGAGAG-AAGAGAGAGAGAG
• chr9-115021283-AAGAGAGAG-AAGAGAGAGAGAGAG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_002160.4(TNC):​c.6496-24_6496-17delCTCTCTCT variant causes a intron change. The variant allele was found at a frequency of 0.0000454 in 1,102,214 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00010 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000037 (0 hom.)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.13

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 15 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNC	NM_002160.4	c.6496-24_6496-17delCTCTCTCT		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.6496-24_6496-17delCTCTCTCT		intron_variant	Intron 27 of 27	1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.000100 AC: 15 AN: 149628 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000295

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000667

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000297

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000367 AC: 35 AN: 952586 Hom.: 0 AF XY: 0.0000274 AC XY: 13 AN XY: 474310

Gnomad4 AFR exome AF: 0.000599

Gnomad4 AMR exome AF: 0.0000356

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000731

Gnomad4 SAS exome AF: 0.0000175

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000221

Gnomad4 OTH exome AF: 0.0000255

GnomAD4 genome AF: 0.000100 AC: 15 AN: 149628 Hom.: 0 Cov.: 32 AF XY: 0.0000960 AC XY: 7 AN XY: 72944

Gnomad4 AFR AF: 0.000295

Gnomad4 AMR AF: 0.0000667

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000297

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs766737426; hg19: chr9-117783562;