9-114865289-G-T

Variant names:

• chr9-114865289-G-T
• rs7866342
• ENST00000648852.1:n.49+14273G>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.49+14273G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,146 control chromosomes in the GnomAD database, including 46,512 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 0.77 (46512 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 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.49+14273G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117643 AN: 152028 Hom.: 46442 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.774 AC: 117778 AN: 152146 Hom.: 46512 Cov.: 32 AF XY: 0.776 AC XY: 57683 AN XY: 74368

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.744

Alfa AF: 0.710 Hom.: 76385

Bravo AF: 0.782

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.045
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7866342; hg19: chr9-117627569;