9-115090243-T-C

Position:

• chr9-115090243-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002160.4(TNC):​c.457+319A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,932 control chromosomes in the GnomAD database, including 8,166 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (8166 hom., cov: 31)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

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]

LOC124902255 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNC	NM_002160.4	c.457+319A>G		intron_variant		ENST00000350763.9
LOC124902255	XR_007061746.1	n.64+2789T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNC	ENST00000350763.9	c.457+319A>G		intron_variant		1	NM_002160.4	P1
DELEC1	ENST00000649121.1	n.322+2789T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49475 AN: 151814 Hom.: 8145 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.326 AC: 49548 AN: 151932 Hom.: 8166 Cov.: 31 AF XY: 0.326 AC XY: 24219 AN XY: 74258

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.348

Alfa AF: 0.323 Hom.: 4490

Bravo AF: 0.333

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.61

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: rs1271449; hg19: chr9-117852522;