rs12006094

Variant names:

• chr9-115009031-T-C
• rs12006094
• ENST00000648852.1:n.276+39370T>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+39370T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,078 control chromosomes in the GnomAD database, including 2,048 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 0.16 (2048 hom., cov: 31)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 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+39370T>C		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+39370T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23868 AN: 151960 Hom.: 2047 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.157 AC: 23868 AN: 152078 Hom.: 2048 Cov.: 31 AF XY: 0.152 AC XY: 11285 AN XY: 74352

African (AFR) AF: 0.132 AC: 5480 AN: 41478

American (AMR) AF: 0.103 AC: 1575 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 238 AN: 3472

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5164

South Asian (SAS) AF: 0.120 AC: 578 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1991 AN: 10584

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13420 AN: 67960

Other (OTH) AF: 0.127 AC: 267 AN: 2110

Alfa AF: 0.176 Hom.: 4201

Bravo AF: 0.149

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.74
DANN	Benign	0.47
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs12006094; hg19: chr9-117771310;