rs10117421

Positions:

• chr9-115016090-A-C
• chr9-115016090-A-T

Variant summary

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

The ENST00000649121.1(DELEC1):​n.78+46429A>C 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 0.149 in 152,128 control chromosomes in the GnomAD database, including 1,823 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 0.15 (1823 hom., cov: 33)
• Consequence: DELEC1 ENST00000649121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000649121.1	n.78+46429A>C		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000648852.1	n.276+46429A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22612 AN: 152010 Hom.: 1820 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.00696

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.149 AC: 22632 AN: 152128 Hom.: 1823 Cov.: 33 AF XY: 0.147 AC XY: 10960 AN XY: 74390

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.00678

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.172

Alfa AF: 0.145 Hom.: 2343

Bravo AF: 0.150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10117421; hg19: chr9-117778369; COSMIC: COSV60782584;