rs1407309

Positions:

• chr9-114889500-G-A
• chr9-114889500-G-T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.50-31950G>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 0.549 in 151,480 control chromosomes in the GnomAD database, including 24,439 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 0.55 (24439 hom., cov: 29)
• Consequence: DELEC1 ENST00000648852.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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.50-31950G>A		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000649565.1	n.225+4192G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83014 AN: 151364 Hom.: 24400 Cov.: 29

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.549 AC: 83112 AN: 151480 Hom.: 24439 Cov.: 29 AF XY: 0.551 AC XY: 40773 AN XY: 73940

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.510

Alfa AF: 0.445 Hom.: 11560

Bravo AF: 0.571

Asia WGS AF: 0.481 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1407309; hg19: chr9-117651780;