rs12156617

Positions:

• chr9-115016064-C-T

Variant summary

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

The ENST00000649121.1(DELEC1):​n.78+46403C>T 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 0.127 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 ENST00000649121.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000649121.1	n.78+46403C>T		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000648852.1	n.276+46403C>T		intron_variant, non_coding_transcript_variant

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;