rs998410

Variant names:

• chr9-114860394-G-T
• rs998410
• ENST00000648852.1:n.49+9378G>T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.49+9378G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 152,236 control chromosomes in the GnomAD database, including 793 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 0.064 (793 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.802
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.49+9378G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9793 AN: 152116 Hom.: 792 Cov.: 33

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0645 AC: 9817 AN: 152236 Hom.: 793 Cov.: 33 AF XY: 0.0728 AC XY: 5418 AN XY: 74442

African (AFR) AF: 0.0348 AC: 1448 AN: 41552

American (AMR) AF: 0.172 AC: 2625 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1542 AN: 5176

South Asian (SAS) AF: 0.0600 AC: 290 AN: 4830

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10594

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2086 AN: 68016

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0669 Hom.: 301

Bravo AF: 0.0713

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.52
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs998410; hg19: chr9-117622674;