rs10817691

Variant names:

• chr9-114957982-A-C
• rs10817691
• ENST00000648852.1:n.199-11602A>C

Variant summary

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

The ENST00000648852.1(DELEC1):​n.199-11602A>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 2 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]

ENSG00000299819 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648852.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000648852.1		n.199-11602A>C		intron	N/A
	DELEC1	ENST00000649565.1		n.226-11602A>C		intron	N/A
	ENSG00000299819	ENST00000766667.1		n.88-4359T>G		intron	N/A

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

African (AFR) AF: 0.523 AC: 21699 AN: 41486

American (AMR) AF: 0.406 AC: 6216 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2281 AN: 5164

South Asian (SAS) AF: 0.512 AC: 2471 AN: 4826

European-Finnish (FIN) AF: 0.458 AC: 4844 AN: 10568

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31517 AN: 67958

Other (OTH) AF: 0.472 AC: 998 AN: 2114

Alfa AF: 0.464 Hom.: 22444

Bravo AF: 0.470

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10817691; hg19: chr9-117720262;