rs1591420

Variant names:

• chr9-115140190-C-G
• rs1591420
• ENST00000649121.1:n.323-1464C>G

Variant summary

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

The ENST00000649121.1(DELEC1):​n.323-1464C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 151,980 control chromosomes in the GnomAD database, including 359 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 0.054 (359 hom., cov: 32)
• Consequence: DELEC1 ENST00000649121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• 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]

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 (AMR) allele frequency at 95% confidence interval = 0.0668 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	ENST00000649121.1	n.323-1464C>G		intron_variant	Intron 3 of 6
DELEC1	ENST00000825162.1	n.717-1464C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8245 AN: 151868 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.0390

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0101

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0543 AC: 8248 AN: 151980 Hom.: 359 Cov.: 32 AF XY: 0.0590 AC XY: 4381 AN XY: 74258

African (AFR) AF: 0.0129 AC: 534 AN: 41504

American (AMR) AF: 0.0703 AC: 1073 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3466

East Asian (EAS) AF: 0.0634 AC: 327 AN: 5154

South Asian (SAS) AF: 0.0388 AC: 187 AN: 4814

European-Finnish (FIN) AF: 0.163 AC: 1718 AN: 10542

Middle Eastern (MID) AF: 0.00725 AC: 2 AN: 276

European-Non Finnish (NFE) AF: 0.0593 AC: 4028 AN: 67934

Other (OTH) AF: 0.0412 AC: 87 AN: 2114

Alfa AF: 0.0611 Hom.: 53

Bravo AF: 0.0470

Asia WGS AF: 0.0490 AC: 172 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.063
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1591420; hg19: chr9-117902469;