chr9-114934056-C-T

Variant names:

• chr9-114934056-C-T
• rs726657
• ENST00000648852.1:n.198+12458C>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.198+12458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,084 control chromosomes in the GnomAD database, including 19,778 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 0.50 (19778 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 17 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 (AFR) allele frequency at 95% confidence interval = 0.667 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.198+12458C>T		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-35528C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75216 AN: 151962 Hom.: 19735 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.495 AC: 75323 AN: 152084 Hom.: 19778 Cov.: 32 AF XY: 0.494 AC XY: 36761 AN XY: 74342

African (AFR) AF: 0.674 AC: 27957 AN: 41490

American (AMR) AF: 0.515 AC: 7873 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1325 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2005 AN: 4810

European-Finnish (FIN) AF: 0.414 AC: 4373 AN: 10574

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28726 AN: 67966

Other (OTH) AF: 0.463 AC: 977 AN: 2112

Alfa AF: 0.452 Hom.: 43924

Bravo AF: 0.508

Asia WGS AF: 0.424 AC: 1471 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	0.99
DANN	Benign	0.54
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs726657; hg19: chr9-117696336;