rs3814957

chr9-115330728-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DELEC1	NR_163556.1	n.458+24732T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000484171.2	n.979T>C		non_coding_transcript_exon_variant	5/5	1
DELEC1	ENST00000374016.5	n.458+24732T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000646338.1	n.276-5294A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 NFE exome AF: 0.583

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.333

Alfa AF: 0.322 Hom.: 8099

Bravo AF: 0.336

Asia WGS AF: 0.359 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.6
Dann	Benign	0.83

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

Publications

LitVar

Other links and lift over

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