rs4978620

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649121.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000649121.1		n.323-442T>C		intron	N/A
	DELEC1	ENST00000825162.1		n.717-442T>C		intron	N/A

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

African (AFR) AF: 0.266 AC: 10727 AN: 40330

American (AMR) AF: 0.272 AC: 4021 AN: 14788

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1350 AN: 3448

East Asian (EAS) AF: 0.498 AC: 2534 AN: 5084

South Asian (SAS) AF: 0.329 AC: 1507 AN: 4574

European-Finnish (FIN) AF: 0.257 AC: 2621 AN: 10190

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20599 AN: 67478

Other (OTH) AF: 0.295 AC: 600 AN: 2034

Alfa AF: 0.305 Hom.: 899

Bravo AF: 0.299

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	15
DANN	Benign	0.47
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4978620; hg19: chr9-117903491;