chr9-115002569-C-T

Variant names:

• chr9-115002569-C-T
• rs4978617
• ENST00000648852.1:n.276+32908C>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+32908C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,098 control chromosomes in the GnomAD database, including 29,750 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 0.62 (29750 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 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	ENST00000648852.1	n.276+32908C>T		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+32908C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93496 AN: 151978 Hom.: 29738 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.615 AC: 93549 AN: 152098 Hom.: 29750 Cov.: 32 AF XY: 0.616 AC XY: 45796 AN XY: 74366

African (AFR) AF: 0.461 AC: 19130 AN: 41482

American (AMR) AF: 0.552 AC: 8431 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3117 AN: 5160

South Asian (SAS) AF: 0.673 AC: 3251 AN: 4828

European-Finnish (FIN) AF: 0.729 AC: 7716 AN: 10584

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47676 AN: 67986

Other (OTH) AF: 0.583 AC: 1227 AN: 2106

Alfa AF: 0.643 Hom.: 5646

Bravo AF: 0.589

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4978617; hg19: chr9-117764849; COSMIC: COSV60395732;