ENST00000374016.5:n.533-4909T>C

Variant names:

• chr9-115395450-T-C
• rs10982724
• ENST00000374016.5:n.533-4909T>C

Variant summary

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

The ENST00000374016.5(DELEC1):​n.533-4909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,764 control chromosomes in the GnomAD database, including 2,700 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 0.17 (2700 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 5 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]

ENSG00000228714 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2	n.533-4909T>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.533-4909T>C		intron_variant	Intron 5 of 7	1
ENSG00000228714	ENST00000646338.1	n.276-70016A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26073 AN: 151646 Hom.: 2696 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0595

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.172 AC: 26104 AN: 151764 Hom.: 2700 Cov.: 32 AF XY: 0.174 AC XY: 12897 AN XY: 74186

African (AFR) AF: 0.279 AC: 11501 AN: 41292

American (AMR) AF: 0.145 AC: 2215 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0595 AC: 206 AN: 3464

East Asian (EAS) AF: 0.318 AC: 1635 AN: 5144

South Asian (SAS) AF: 0.106 AC: 511 AN: 4800

European-Finnish (FIN) AF: 0.176 AC: 1856 AN: 10552

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7783 AN: 67934

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.128 Hom.: 6462

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.42
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: rs10982724; hg19: chr9-118157729;