ENST00000648852.1:n.50-31950G>A

Variant names:

• chr9-114889500-G-A
• rs1407309
• ENST00000648852.1:n.50-31950G>A

Variant summary

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

The ENST00000648852.1(DELEC1):​n.50-31950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,480 control chromosomes in the GnomAD database, including 24,439 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 0.55 (24439 hom., cov: 29)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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.50-31950G>A		intron_variant	Intron 1 of 5
DELEC1	ENST00000649565.1	n.225+4192G>A		intron_variant	Intron 1 of 1
DELEC1	ENST00000815338.1	n.228+4192G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83014 AN: 151364 Hom.: 24400 Cov.: 29

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.549 AC: 83112 AN: 151480 Hom.: 24439 Cov.: 29 AF XY: 0.551 AC XY: 40773 AN XY: 73940

African (AFR) AF: 0.753 AC: 31102 AN: 41316

American (AMR) AF: 0.640 AC: 9746 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1602 AN: 3458

East Asian (EAS) AF: 0.332 AC: 1682 AN: 5068

South Asian (SAS) AF: 0.431 AC: 2066 AN: 4788

European-Finnish (FIN) AF: 0.490 AC: 5135 AN: 10474

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30138 AN: 67850

Other (OTH) AF: 0.510 AC: 1070 AN: 2098

Alfa AF: 0.468 Hom.: 16996

Bravo AF: 0.571

Asia WGS AF: 0.481 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1407309; hg19: chr9-117651780;