rs10817727

Variant names:

• chr9-115217131-A-G
• rs10817727
• ENST00000374016.5:n.52-16045A>G

Variant summary

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

The ENST00000374016.5(DELEC1):​n.52-16045A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,120 control chromosomes in the GnomAD database, including 1,553 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 0.14 (1553 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 4 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]

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 = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000374016.5. 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
	DELEC1	NR_163556.2		n.52-16045A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000374016.5	TSL:1	n.52-16045A>G		intron	N/A
	DELEC1	ENST00000484171.2	TSL:1	n.146+7056A>G		intron	N/A
	DELEC1	ENST00000647970.1		n.138+7056A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20632 AN: 152002 Hom.: 1555 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.136 AC: 20639 AN: 152120 Hom.: 1553 Cov.: 32 AF XY: 0.134 AC XY: 9941 AN XY: 74352

African (AFR) AF: 0.197 AC: 8158 AN: 41488

American (AMR) AF: 0.129 AC: 1970 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3470

East Asian (EAS) AF: 0.103 AC: 534 AN: 5160

South Asian (SAS) AF: 0.105 AC: 505 AN: 4810

European-Finnish (FIN) AF: 0.0885 AC: 939 AN: 10608

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7401 AN: 67994

Other (OTH) AF: 0.168 AC: 353 AN: 2106

Alfa AF: 0.123 Hom.: 2351

Bravo AF: 0.141

Asia WGS AF: 0.117 AC: 404 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.55
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10817727;

hg19: chr9-117979410;