rs1999223

Variant names:

• chr9-115013051-G-T
• rs1999223
• ENST00000648852.1:n.276+43390G>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+43390G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,088 control chromosomes in the GnomAD database, including 2,918 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 0.19 (2918 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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+43390G>T		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+43390G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29251 AN: 151970 Hom.: 2917 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.192 AC: 29262 AN: 152088 Hom.: 2918 Cov.: 32 AF XY: 0.193 AC XY: 14364 AN XY: 74324

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.183

Alfa AF: 0.213 Hom.: 455

Bravo AF: 0.179

Asia WGS AF: 0.220 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999223; hg19: chr9-117775330;