NM_002160.4:c.2132-247A>C

Variant names:

• chr9-115083054-T-G
• rs1757106
• NM_002160.4:c.2132-247A>C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002160.4(TNC):​c.2132-247A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,054 control chromosomes in the GnomAD database, including 24,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.56 (24559 hom., cov: 33)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.89

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 9-115083054-T-G is Benign according to our data. Variant chr9-115083054-T-G is described in ClinVar as [Benign]. Clinvar id is 1238384.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNC	NM_002160.4	c.2132-247A>C		intron_variant	Intron 4 of 27	ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9	c.2132-247A>C		intron_variant	Intron 4 of 27	1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85649 AN: 151936 Hom.: 24520 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.564 AC: 85748 AN: 152054 Hom.: 24559 Cov.: 33 AF XY: 0.562 AC XY: 41773 AN XY: 74338

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.589

Alfa AF: 0.544 Hom.: 45737

Bravo AF: 0.577

Asia WGS AF: 0.479 AC: 1670 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 29, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.66

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: rs1757106; hg19: chr9-117845333;