rs1591420

chr9-115140190-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649121.1(DELEC1):n.323-1464C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000649121.1	n.323-1464C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.0634

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.0412

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1591420; hg19: chr9-117902469;