chr9-115029105-C-T

Position:

• chr9-115029105-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_002160.4(TNC):​c.6169+255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0086 in 144,846 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0086 (9 hom., cov: 30)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.996

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 9-115029105-C-T is Benign according to our data. Variant chr9-115029105-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1316783.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 1245 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNC	NM_002160.4	c.6169+255G>A		intron_variant		ENST00000350763.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNC	ENST00000350763.9	c.6169+255G>A		intron_variant		1	NM_002160.4	P1
DELEC1	ENST00000649121.1	n.79-55150C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00860 AC: 1245 AN: 144846 Hom.: 9 Cov.: 30

Gnomad AFR AF: 0.00216

Gnomad AMI AF: 0.00443

Gnomad AMR AF: 0.00167

Gnomad ASJ AF: 0.00145

Gnomad EAS AF: 0.000204

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.00694

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.00556

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

GnomAD4 genome AF: 0.00860 AC: 1245 AN: 144846 Hom.: 9 Cov.: 30 AF XY: 0.00832 AC XY: 581 AN XY: 69852

Gnomad4 AFR AF: 0.00215

Gnomad4 AMR AF: 0.00166

Gnomad4 ASJ AF: 0.00145

Gnomad4 EAS AF: 0.000204

Gnomad4 SAS AF: 0.0103

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.0147

Gnomad4 OTH AF: 0.00552

Alfa AF: 0.0143 Hom.: 3

Bravo AF: 0.00716

Asia WGS AF: 0.00376 AC: 13 AN: 3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.44

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: rs183619566; hg19: chr9-117791384;