ENST00000484171.2:n.979T>C

Variant names:

• chr9-115330728-T-C
• rs3814957
• ENST00000484171.2:n.979T>C

Variant summary

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

The ENST00000484171.2(DELEC1):​n.979T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,174 control chromosomes in the GnomAD database, including 8,534 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 0.33 (8532 hom., cov: 33)
  • Exomes 𝑓: 0.64 (2 hom.)
• Consequence: DELEC1 ENST00000484171.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 1 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]

ENSG00000228714 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484171.2. 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.458+24732T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000484171.2	TSL:1	n.979T>C		non_coding_transcript_exon	Exon 5 of 5
	DELEC1	ENST00000374016.5	TSL:1	n.458+24732T>C		intron	N/A
	DELEC1	ENST00000807886.1		n.872T>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50698 AN: 152042 Hom.: 8523 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.643 AC: 9 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.643 AC XY: 9 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.583 AC: 7 AN: 12

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.333 AC: 50730 AN: 152160 Hom.: 8532 Cov.: 33 AF XY: 0.337 AC XY: 25050 AN XY: 74388

African (AFR) AF: 0.330 AC: 13698 AN: 41492

American (AMR) AF: 0.395 AC: 6034 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1758 AN: 5164

South Asian (SAS) AF: 0.382 AC: 1845 AN: 4828

European-Finnish (FIN) AF: 0.340 AC: 3604 AN: 10592

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21497 AN: 68008

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.323 Hom.: 10595

Bravo AF: 0.336

Asia WGS AF: 0.359 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3814957; hg19: chr9-118093007; COSMIC: COSV64982270;