rs4452883

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648852.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000648852.1		n.276+47634C>T		intron	N/A
	DELEC1	ENST00000649121.1		n.78+47634C>T		intron	N/A

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

African (AFR) AF: 0.0903 AC: 3748 AN: 41484

American (AMR) AF: 0.198 AC: 3025 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 525 AN: 3462

East Asian (EAS) AF: 0.154 AC: 793 AN: 5158

South Asian (SAS) AF: 0.156 AC: 750 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3507 AN: 10546

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18794 AN: 67986

Other (OTH) AF: 0.209 AC: 441 AN: 2114

Alfa AF: 0.223 Hom.: 556

Bravo AF: 0.198

Asia WGS AF: 0.150 AC: 521 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.46
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs4452883; hg19: chr9-117779574;