rs4452883

Variant names:

• chr9-115017295-C-T
• rs4452883
• ENST00000648852.1:n.276+47634C>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+47634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,048 control chromosomes in the GnomAD database, including 3,827 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 0.21 (3827 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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]

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 (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.276+47634C>T		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+47634C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31879 AN: 151930 Hom.: 3828 Cov.: 33

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31876 AN: 152048 Hom.: 3827 Cov.: 33 AF XY: 0.210 AC XY: 15576 AN XY: 74310

Gnomad4 AFR AF: 0.0903

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.209

Alfa AF: 0.228 Hom.: 552

Bravo AF: 0.198

Asia WGS AF: 0.150 AC: 521 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4452883; hg19: chr9-117779574;