ENST00000649121.1:n.323-442T>C

Variant names:

• chr9-115141212-T-C
• rs4978620
• ENST00000649121.1:n.323-442T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649121.1(DELEC1):​n.323-442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 149,128 control chromosomes in the GnomAD database, including 6,794 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 0.30 (6794 hom., cov: 28)
• Consequence: DELEC1 ENST00000649121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 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	ENST00000649121.1	n.323-442T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.298 AC: 44447 AN: 149010 Hom.: 6788 Cov.: 28

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.298 AC: 44459 AN: 149128 Hom.: 6794 Cov.: 28 AF XY: 0.298 AC XY: 21582 AN XY: 72542

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.295

Alfa AF: 0.306 Hom.: 866

Bravo AF: 0.299

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	15
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4978620; hg19: chr9-117903491;