9-115019377-C-T

Variant names:

• chr9-115019377-C-T
• rs11787664
• ENST00000648852.1:n.277-49619C>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.277-49619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,004 control chromosomes in the GnomAD database, including 13,508 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 0.40 (13508 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528

Genes affected

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]

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNC	NM_002160.4	c.*1780G>A		downstream_gene_variant		ENST00000350763.9	NP_002151.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.277-49619C>T		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+49716C>T		intron_variant	Intron 1 of 6
TNC	ENST00000350763.9	c.*1780G>A		downstream_gene_variant		1	NM_002160.4	ENSP00000265131.4

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61320 AN: 151886 Hom.: 13508 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.404 AC: 61336 AN: 152004 Hom.: 13508 Cov.: 32 AF XY: 0.404 AC XY: 30057 AN XY: 74308

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.392

Alfa AF: 0.457 Hom.: 21943

Bravo AF: 0.379

Asia WGS AF: 0.367 AC: 1278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.4
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11787664; hg19: chr9-117781656;