chr9-114934654-C-A

Variant names:

• chr9-114934654-C-A
• rs1322059
• ENST00000648852.1:n.198+13056C>A

Variant summary

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

The ENST00000648852.1(DELEC1):​n.198+13056C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,030 control chromosomes in the GnomAD database, including 9,650 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 0.35 (9650 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.434 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+13056C>A		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-34930C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52707 AN: 151912 Hom.: 9641 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.347 AC: 52739 AN: 152030 Hom.: 9650 Cov.: 32 AF XY: 0.350 AC XY: 25998 AN XY: 74288

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.350

Alfa AF: 0.362 Hom.: 1279

Bravo AF: 0.344

Asia WGS AF: 0.378 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322059; hg19: chr9-117696934;