ENST00000374016.5:n.52-4263G>A

Variant names:

• chr9-115228913-G-A
• rs955387
• ENST00000374016.5:n.52-4263G>A

Variant summary

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

The ENST00000374016.5(DELEC1):​n.52-4263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,126 control chromosomes in the GnomAD database, including 413 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 0.067 (413 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2	n.52-4263G>A		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.52-4263G>A		intron_variant	Intron 1 of 7	1
DELEC1	ENST00000484171.2	n.147-4263G>A		intron_variant	Intron 1 of 4	1
DELEC1	ENST00000647970.1	n.139-4263G>A		intron_variant	Intron 1 of 5
DELEC1	ENST00000649121.1	n.659-4263G>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10239 AN: 152008 Hom.: 412 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0673 AC: 10238 AN: 152126 Hom.: 413 Cov.: 32 AF XY: 0.0656 AC XY: 4879 AN XY: 74378

African (AFR) AF: 0.0181 AC: 751 AN: 41498

American (AMR) AF: 0.0817 AC: 1249 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5176

South Asian (SAS) AF: 0.0512 AC: 246 AN: 4804

European-Finnish (FIN) AF: 0.0666 AC: 705 AN: 10584

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0979 AC: 6656 AN: 68004

Other (OTH) AF: 0.0894 AC: 188 AN: 2104

Alfa AF: 0.0763 Hom.: 462

Bravo AF: 0.0664

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.9
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: rs955387; hg19: chr9-117991192;