rs17819305

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002160.4(TNC):​c.4579+3202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 152,254 control chromosomes in the GnomAD database, including 349 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 0.055 ( 349 hom., cov: 33)

Consequence

TNC
NM_002160.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.575
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0884 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TNCNM_002160.4 linkuse as main transcriptc.4579+3202G>A intron_variant ENST00000350763.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TNCENST00000350763.9 linkuse as main transcriptc.4579+3202G>A intron_variant 1 NM_002160.4 P1P24821-1
DELEC1ENST00000649121.1 linkuse as main transcriptn.79-30304C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0555
AC:
8447
AN:
152136
Hom.:
349
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0154
Gnomad AMI
AF:
0.0747
Gnomad AMR
AF:
0.0359
Gnomad ASJ
AF:
0.0251
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0259
Gnomad FIN
AF:
0.0695
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0903
Gnomad OTH
AF:
0.0454
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0554
AC:
8442
AN:
152254
Hom.:
349
Cov.:
33
AF XY:
0.0524
AC XY:
3899
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0154
Gnomad4 AMR
AF:
0.0358
Gnomad4 ASJ
AF:
0.0251
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0255
Gnomad4 FIN
AF:
0.0695
Gnomad4 NFE
AF:
0.0903
Gnomad4 OTH
AF:
0.0449
Alfa
AF:
0.0739
Hom.:
245
Bravo
AF:
0.0512
Asia WGS
AF:
0.0100
AC:
35
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.96
DANN
Benign
0.52

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17819305; hg19: chr9-117816230; API