rs10982634

Variant names:

• chr9-115255821-T-C
• rs10982634
• ENST00000374016.5:n.212+22485T>C

Variant summary

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

The ENST00000374016.5(DELEC1):​n.212+22485T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,240 control chromosomes in the GnomAD database, including 699 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 0.087 (699 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• 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]

ENSG00000234692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2	n.212+22485T>C		intron_variant	Intron 2 of 7
LOC105376233	XR_930267.3	n.153-1428A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.212+22485T>C		intron_variant	Intron 2 of 7	1
DELEC1	ENST00000484171.2	n.307+22485T>C		intron_variant	Intron 2 of 4	1
DELEC1	ENST00000647970.1	n.299+22485T>C		intron_variant	Intron 2 of 5
ENSG00000234692	ENST00000775649.1	n.169-1428A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13175 AN: 152122 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.0197

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0865 AC: 13176 AN: 152240 Hom.: 699 Cov.: 32 AF XY: 0.0891 AC XY: 6629 AN XY: 74422

African (AFR) AF: 0.0197 AC: 817 AN: 41576

American (AMR) AF: 0.103 AC: 1579 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3466

East Asian (EAS) AF: 0.113 AC: 585 AN: 5178

South Asian (SAS) AF: 0.107 AC: 515 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10600

Middle Eastern (MID) AF: 0.128 AC: 37 AN: 290

European-Non Finnish (NFE) AF: 0.109 AC: 7405 AN: 67998

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.102 Hom.: 436

Bravo AF: 0.0803

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.013
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

Other links and lift over

dbSNP: rs10982634; hg19: chr9-118018100;