ENST00000648852.1:n.276+46429A>C

Variant names:

• chr9-115016090-A-C
• rs10117421
• ENST00000648852.1:n.276+46429A>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+46429A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,128 control chromosomes in the GnomAD database, including 1,823 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 0.15 (1823 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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+46429A>C		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+46429A>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22612 AN: 152010 Hom.: 1820 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.00696

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.149 AC: 22632 AN: 152128 Hom.: 1823 Cov.: 33 AF XY: 0.147 AC XY: 10960 AN XY: 74390

African (AFR) AF: 0.180 AC: 7484 AN: 41504

American (AMR) AF: 0.124 AC: 1894 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3470

East Asian (EAS) AF: 0.00678 AC: 35 AN: 5164

South Asian (SAS) AF: 0.128 AC: 619 AN: 4826

European-Finnish (FIN) AF: 0.117 AC: 1243 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9924 AN: 67968

Other (OTH) AF: 0.172 AC: 361 AN: 2102

Alfa AF: 0.146 Hom.: 2998

Bravo AF: 0.150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10117421; hg19: chr9-117778369; COSMIC: COSV60782584;