rs17239726

Variant names:

• chr9-115009233-G-A
• rs17239726
• ENST00000648852.1:n.276+39572G>A

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+39572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,162 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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+39572G>A		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+39572G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21801 AN: 152044 Hom.: 1736 Cov.: 33

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.143 AC: 21795 AN: 152162 Hom.: 1736 Cov.: 33 AF XY: 0.142 AC XY: 10563 AN XY: 74376

Gnomad4 AFR AF: 0.0751

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.116

Alfa AF: 0.172 Hom.: 1073

Bravo AF: 0.134

Asia WGS AF: 0.207 AC: 718 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17239726; hg19: chr9-117771512;