rs726657

chr9-114934056-C-T

Variant summary

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

The ENST00000648852.1(DELEC1):n.198+12458C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,084 control chromosomes in the GnomAD database, including 19,778 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 0.50 (19778 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000648852.1	n.198+12458C>T		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000649565.1	n.226-35528C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75216 AN: 151962 Hom.: 19735 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.495 AC: 75323 AN: 152084 Hom.: 19778 Cov.: 32 AF XY: 0.494 AC XY: 36761 AN XY: 74342

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.463

Alfa AF: 0.433 Hom.: 24543

Bravo AF: 0.508

Asia WGS AF: 0.424 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.99
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726657; hg19: chr9-117696336;