rs10817691

Positions:

• chr9-114957982-A-C

Variant summary

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

The ENST00000648852.1(DELEC1):​n.199-11602A>C 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 0.472 in 152,084 control chromosomes in the GnomAD database, including 16,976 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 0.47 (16976 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.199-11602A>C		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000649565.1	n.226-11602A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71717 AN: 151966 Hom.: 16953 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.472 AC: 71784 AN: 152084 Hom.: 16976 Cov.: 32 AF XY: 0.470 AC XY: 34909 AN XY: 74346

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.472

Alfa AF: 0.463 Hom.: 17697

Bravo AF: 0.470

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817691; hg19: chr9-117720262;