rs12156617

Variant names:

• chr9-115016064-C-T
• rs12156617
• ENST00000648852.1:n.276+46403C>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+46403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,202 control chromosomes in the GnomAD database, including 2,244 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 0.13 (2244 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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 = 0.307 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.276+46403C>T		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+46403C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19344 AN: 152086 Hom.: 2239 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.0214

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.0569

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.127 AC: 19371 AN: 152202 Hom.: 2244 Cov.: 32 AF XY: 0.123 AC XY: 9141 AN XY: 74408

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0214

Gnomad4 NFE AF: 0.0569

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0950 Hom.: 158

Bravo AF: 0.140

Asia WGS AF: 0.0470 AC: 165 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	6.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12156617; hg19: chr9-117778343;