chr9-115117870-A-G

Position:

• chr9-115117870-A-G

Variant summary

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

The NM_002160.4(TNC):​c.-137+112T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,026 control chromosomes in the GnomAD database, including 6,190 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 0.28 (6190 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.45

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNC	NM_002160.4	c.-137+112T>C		intron_variant		ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNC	ENST00000350763.9	c.-137+112T>C		intron_variant		1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42575 AN: 151906 Hom.: 6183 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.273

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.280 AC: 42579 AN: 152024 Hom.: 6190 Cov.: 32 AF XY: 0.280 AC XY: 20794 AN XY: 74314

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.278

Alfa AF: 0.179 Hom.: 370

Bravo AF: 0.275

Asia WGS AF: 0.312 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.020
DANN	Benign	0.35

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: rs3748166; hg19: chr9-117880149;