rs3789870

Positions:

• chr9-115072997-A-G
• chr9-115072997-A-T

Variant summary

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

The NM_002160.4(TNC):​c.3214+606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,038 control chromosomes in the GnomAD database, including 47,385 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 0.78 (47385 hom., cov: 31)
• Consequence: TNC NM_002160.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.00

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]

LOC124902256 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNC	NM_002160.4	c.3214+606T>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.3214+606T>C		intron_variant		1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119133 AN: 151920 Hom.: 47320 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.784 AC: 119258 AN: 152038 Hom.: 47385 Cov.: 31 AF XY: 0.783 AC XY: 58162 AN XY: 74312

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.785

Alfa AF: 0.701 Hom.: 2068

Bravo AF: 0.786

Asia WGS AF: 0.647 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3789870; hg19: chr9-117835276;