9-115078463-G-C

Position:

• chr9-115078463-G-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.2405-251C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 150,400 control chromosomes in the GnomAD database, including 20,954 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.52 (20954 hom., cov: 27)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.28

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:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 9-115078463-G-C is Benign according to our data. Variant chr9-115078463-G-C is described in ClinVar as [Benign]. Clinvar id is 1280678.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNC	NM_002160.4	c.2405-251C>G		intron_variant		ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9	c.2405-251C>G		intron_variant		1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.523 AC: 78567 AN: 150286 Hom.: 20945 Cov.: 27

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.523 AC: 78602 AN: 150400 Hom.: 20954 Cov.: 27 AF XY: 0.521 AC XY: 38217 AN XY: 73302

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.472

Alfa AF: 0.549 Hom.: 2818

Bravo AF: 0.510

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.63

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: rs1330349; hg19: chr9-117840742; COSMIC: COSV60789776; COSMIC: COSV60789776;