9-115213585-A-G

Variant names:

• chr9-115213585-A-G
• rs10982611
• ENST00000374016.5:n.52-19591A>G

Variant summary

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

The ENST00000374016.5(DELEC1):​n.52-19591A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,940 control chromosomes in the GnomAD database, including 8,512 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 0.32 (8512 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2	n.52-19591A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.52-19591A>G		intron_variant	Intron 1 of 7	1
DELEC1	ENST00000484171.2	n.146+3510A>G		intron_variant	Intron 1 of 4	1
DELEC1	ENST00000647970.1	n.138+3510A>G		intron_variant	Intron 1 of 5
DELEC1	ENST00000649121.1	n.659-19591A>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48764 AN: 151822 Hom.: 8508 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.321 AC: 48761 AN: 151940 Hom.: 8512 Cov.: 32 AF XY: 0.320 AC XY: 23758 AN XY: 74252

African (AFR) AF: 0.184 AC: 7616 AN: 41448

American (AMR) AF: 0.316 AC: 4822 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1279 AN: 5140

South Asian (SAS) AF: 0.445 AC: 2139 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3562 AN: 10540

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26624 AN: 67960

Other (OTH) AF: 0.375 AC: 790 AN: 2108

Alfa AF: 0.374 Hom.: 47671

Bravo AF: 0.310

Asia WGS AF: 0.330 AC: 1146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10982611; hg19: chr9-117975864; COSMIC: COSV64982080;