rs873211

Variant names:

• chr9-114973665-G-C
• rs873211
• ENST00000648852.1:n.276+4004G>C

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+4004G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,228 control chromosomes in the GnomAD database, including 1,099 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 0.10 (1099 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• 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]

ENSG00000299819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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.276+4004G>C		intron	N/A
	DELEC1	ENST00000649121.1		n.78+4004G>C		intron	N/A
	ENSG00000299819	ENST00000766667.1		n.88-20042C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15375 AN: 152110 Hom.: 1099 Cov.: 33

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.101 AC: 15373 AN: 152228 Hom.: 1099 Cov.: 33 AF XY: 0.101 AC XY: 7511 AN XY: 74430

African (AFR) AF: 0.0248 AC: 1032 AN: 41546

American (AMR) AF: 0.0686 AC: 1049 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3468

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5186

South Asian (SAS) AF: 0.118 AC: 572 AN: 4832

European-Finnish (FIN) AF: 0.194 AC: 2058 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10088 AN: 68008

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.129 Hom.: 187

Bravo AF: 0.0876

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.81
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs873211; hg19: chr9-117735945;