NM_002160.4:c.6496-7_6496-6delTT

Variant names:

• chr9-115021272-TAA-T
• rs5900112
• NM_002160.4:c.6496-7_6496-6delTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002160.4(TNC):​c.6496-7_6496-6delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00197 in 1,326,472 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. 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 0.0000069 (0 hom., cov: 24)
  • Exomes 𝑓: 0.0022 (0 hom.)
• Consequence: TNC NM_002160.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• Publications: 2 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: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNC	NM_002160.4	MANE Select	c.6496-7_6496-6delTT		splice_region intron	N/A	NP_002151.2	P24821-1
	TNC	NM_001439065.1		c.7045-7_7045-6delTT		splice_region intron	N/A	NP_001425994.1
	TNC	NM_001439066.1		c.7045-7_7045-6delTT		splice_region intron	N/A	NP_001425995.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNC	ENST00000350763.9	TSL:1 MANE Select	c.6496-7_6496-6delTT		splice_region intron	N/A	ENSP00000265131.4	P24821-1
	TNC	ENST00000423613.6	TSL:1	c.5677-7_5677-6delTT		splice_region intron	N/A	ENSP00000411406.2	E9PC84
	TNC	ENST00000542877.6	TSL:1	c.5407-7_5407-6delTT		splice_region intron	N/A	ENSP00000442242.1	F5H7V9

Frequencies

GnomAD3 genomes AF: 0.00000693 AC: 1 AN: 144338 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000108

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00287 AC: 464 AN: 161918 AF XY: 0.00277

Gnomad AFR exome AF: 0.000661

Gnomad AMR exome AF: 0.00357

Gnomad ASJ exome AF: 0.00276

Gnomad EAS exome AF: 0.00144

Gnomad FIN exome AF: 0.00520

Gnomad NFE exome AF: 0.00277

Gnomad OTH exome AF: 0.00372

GnomAD4 exome AF: 0.00221 AC: 2616 AN: 1182134 Hom.: 0 AF XY: 0.00211 AC XY: 1240 AN XY: 588662

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000773 AC: 19 AN: 24578

American (AMR) AF: 0.00298 AC: 97 AN: 32550

Ashkenazi Jewish (ASJ) AF: 0.00131 AC: 26 AN: 19812

East Asian (EAS) AF: 0.000547 AC: 17 AN: 31074

South Asian (SAS) AF: 0.00132 AC: 86 AN: 64978

European-Finnish (FIN) AF: 0.00336 AC: 145 AN: 43140

Middle Eastern (MID) AF: 0.00115 AC: 5 AN: 4344

European-Non Finnish (NFE) AF: 0.00232 AC: 2123 AN: 913440

Other (OTH) AF: 0.00203 AC: 98 AN: 48218

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.00000693 AC: 1 AN: 144338 Hom.: 0 Cov.: 24 AF XY: 0.0000143 AC XY: 1 AN XY: 69928

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 38696

American (AMR) AF: 0.00 AC: 0 AN: 14498

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3372

East Asian (EAS) AF: 0.00 AC: 0 AN: 4978

South Asian (SAS) AF: 0.00 AC: 0 AN: 4502

European-Finnish (FIN) AF: 0.000108 AC: 1 AN: 9226

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 65928

Other (OTH) AF: 0.00 AC: 0 AN: 1950

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00332 Hom.: 178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.54
Mutation Taster		=99/1	polymorphism

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: rs5900112; hg19: chr9-117783551;