rs1999223

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000648852.1		n.276+43390G>T		intron	N/A
	DELEC1	ENST00000649121.1		n.78+43390G>T		intron	N/A

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

African (AFR) AF: 0.147 AC: 6105 AN: 41482

American (AMR) AF: 0.133 AC: 2028 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.192 AC: 993 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4818

European-Finnish (FIN) AF: 0.226 AC: 2392 AN: 10568

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15292 AN: 67962

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.211 Hom.: 466

Bravo AF: 0.179

Asia WGS AF: 0.220 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.33
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1999223; hg19: chr9-117775330;