rs1322059

Positions:

• chr9-114934654-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.198+13056C>A		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000649565.1	n.226-34930C>A		intron_variant, non_coding_transcript_variant

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;