ENST00000648852.1:n.276+47714G>C

Variant names:

• chr9-115017375-G-C
• rs12555312
• ENST00000648852.1:n.276+47714G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648852.1(DELEC1):​n.276+47714G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 152,264 control chromosomes in the GnomAD database, including 502 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 0.070 (502 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 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+47714G>C		intron	N/A
	DELEC1	ENST00000649121.1		n.78+47714G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10650 AN: 152146 Hom.: 504 Cov.: 33

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0791

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

GnomAD4 genome AF: 0.0699 AC: 10647 AN: 152264 Hom.: 502 Cov.: 33 AF XY: 0.0735 AC XY: 5471 AN XY: 74446

African (AFR) AF: 0.0203 AC: 844 AN: 41550

American (AMR) AF: 0.0549 AC: 840 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.123 AC: 640 AN: 5188

South Asian (SAS) AF: 0.149 AC: 719 AN: 4828

European-Finnish (FIN) AF: 0.0917 AC: 973 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5905 AN: 68012

Other (OTH) AF: 0.0778 AC: 164 AN: 2108

Alfa AF: 0.0355 Hom.: 23

Bravo AF: 0.0624

Asia WGS AF: 0.116 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.69
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs12555312; hg19: chr9-117779654;