9-114935667-G-A

Variant names:

• chr9-114935667-G-A
• rs927375
• ENST00000648852.1:n.198+14069G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648852.1(DELEC1):​n.198+14069G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,032 control chromosomes in the GnomAD database, including 21,483 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 0.52 (21483 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648852.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000648852.1		n.198+14069G>A		intron	N/A
	DELEC1	ENST00000649565.1		n.226-33917G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78490 AN: 151914 Hom.: 21429 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.517 AC: 78610 AN: 152032 Hom.: 21483 Cov.: 32 AF XY: 0.521 AC XY: 38708 AN XY: 74308

African (AFR) AF: 0.681 AC: 28224 AN: 41472

American (AMR) AF: 0.623 AC: 9505 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2132 AN: 5176

South Asian (SAS) AF: 0.438 AC: 2113 AN: 4822

European-Finnish (FIN) AF: 0.465 AC: 4915 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28512 AN: 67944

Other (OTH) AF: 0.488 AC: 1028 AN: 2106

Alfa AF: 0.481 Hom.: 2316

Bravo AF: 0.539

Asia WGS AF: 0.499 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.87
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs927375; hg19: chr9-117697947;