Variant 9-115021283-AAG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_002160.4(TNC):c.6496-18_6496-17del variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.012 in 1,040,288 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)

Exomes 𝑓: 0.014 ( 0 hom. )

Consequence

TNC
NM_002160.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.13

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]

TNC links:

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]

DELEC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-115021283-AAG-A is Benign according to our data. Variant chr9-115021283-AAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316716.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.014 (12424/890600) while in subpopulation AFR AF= 0.0172 (376/21854). AF 95% confidence interval is 0.0158. There are 0 homozygotes in gnomad4_exome. There are 5993 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High AC in GnomAd4 at 33 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNC	NM_002160.4 linkuse as main transcript	c.6496-18_6496-17del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000350763.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNC	ENST00000350763.9 linkuse as main transcript	c.6496-18_6496-17del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_002160.4	P1	P24821-1
DELEC1	ENST00000649121.1 linkuse as main transcript	n.78+51644_78+51645del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.000227

AC:

AN:

149582

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000369

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000267

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000213

Gnomad FIN

AF:

0.000198

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000163

Gnomad OTH

AF:

0.000490

GnomAD3 exomes

AF:

0.00757

AC:

1384

AN:

182926

Hom.:

AF XY:

0.00768

AC XY:

763

AN XY:

99294

show subpopulations

Gnomad AFR exome

AF:

0.00694

Gnomad AMR exome

AF:

0.0105

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00710

Gnomad SAS exome

AF:

0.0119

Gnomad FIN exome

AF:

0.0102

Gnomad NFE exome

AF:

0.00533

Gnomad OTH exome

AF:

0.00796

GnomAD4 exome

AF:

0.0140

AC:

12424

AN:

890600

Hom.:

AF XY:

0.0135

AC XY:

5993

AN XY:

443140

show subpopulations

Gnomad4 AFR exome

AF:

0.0172

Gnomad4 AMR exome

AF:

0.0123

Gnomad4 ASJ exome

AF:

0.0145

Gnomad4 EAS exome

AF:

0.00786

Gnomad4 SAS exome

AF:

0.0133

Gnomad4 FIN exome

AF:

0.00907

Gnomad4 NFE exome

AF:

0.0144

Gnomad4 OTH exome

AF:

0.0133

GnomAD4 genome

AF:

0.000220

AC:

AN:

149688

Hom.:

Cov.:

AF XY:

0.000205

AC XY:

AN XY:

73038

show subpopulations

Gnomad4 AFR

AF:

0.000368

Gnomad4 AMR

AF:

0.000267

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000213

Gnomad4 FIN

AF:

0.000198

Gnomad4 NFE

AF:

0.000149

Gnomad4 OTH

AF:

0.000484

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over