rs726656

Variant names:

• chr9-114934168-A-G
• rs726656
• ENST00000648852.1:n.198+12570A>G

Variant summary

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

The ENST00000648852.1(DELEC1):​n.198+12570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,854 control chromosomes in the GnomAD database, including 9,678 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 (9678 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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 (AMR) allele frequency at 95% confidence interval = 0.435 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+12570A>G		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-35416A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52804 AN: 151736 Hom.: 9669 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.348 AC: 52837 AN: 151854 Hom.: 9678 Cov.: 32 AF XY: 0.351 AC XY: 26051 AN XY: 74208

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.350

Alfa AF: 0.362 Hom.: 1280

Bravo AF: 0.345

Asia WGS AF: 0.378 AC: 1311 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	0.81
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726656; hg19: chr9-117696448;