rs1322060

Variant names:

• chr9-114935380-C-G
• rs1322060
• ENST00000648852.1:n.198+13782C>G

Variant summary

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

The ENST00000648852.1(DELEC1):​n.198+13782C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,012 control chromosomes in the GnomAD database, including 19,336 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 0.49 (19336 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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+13782C>G		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-34204C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74275 AN: 151894 Hom.: 19290 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.489 AC: 74383 AN: 152012 Hom.: 19336 Cov.: 32 AF XY: 0.488 AC XY: 36279 AN XY: 74280

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.459

Alfa AF: 0.461 Hom.: 2124

Bravo AF: 0.503

Asia WGS AF: 0.424 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.071
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322060; hg19: chr9-117697660;