9-115141569-T-C

Variant names:

• chr9-115141569-T-C
• rs2012775
• ENST00000649121.1:n.323-85T>C

Variant summary

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

The ENST00000649121.1(DELEC1):​n.323-85T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,962 control chromosomes in the GnomAD database, including 6,938 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 0.30 (6938 hom., cov: 31)
• Consequence: DELEC1 ENST00000649121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932
• Publications: 10 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649121.1. 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
	DELEC1	NR_163556.2		n.-249T>C		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000649121.1		n.323-85T>C		intron	N/A
	DELEC1	ENST00000825162.1		n.717-85T>C		intron	N/A
	DELEC1	ENST00000374016.5	TSL:1	n.-249T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45467 AN: 151844 Hom.: 6932 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.299 AC: 45479 AN: 151962 Hom.: 6938 Cov.: 31 AF XY: 0.299 AC XY: 22215 AN XY: 74258

African (AFR) AF: 0.268 AC: 11104 AN: 41422

American (AMR) AF: 0.273 AC: 4168 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1358 AN: 3472

East Asian (EAS) AF: 0.499 AC: 2575 AN: 5156

South Asian (SAS) AF: 0.337 AC: 1617 AN: 4802

European-Finnish (FIN) AF: 0.260 AC: 2746 AN: 10564

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20781 AN: 67980

Other (OTH) AF: 0.298 AC: 631 AN: 2114

Alfa AF: 0.295 Hom.: 1820

Bravo AF: 0.299

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.3
DANN	Benign	0.68
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs2012775; hg19: chr9-117903848;