rs873211

Positions:

• chr9-114973665-G-C

Variant summary

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

The ENST00000649121.1(DELEC1):​n.78+4004G>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 0.101 in 152,228 control chromosomes in the GnomAD database, including 1,099 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 0.10 (1099 hom., cov: 33)
• Consequence: DELEC1 ENST00000649121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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.78+4004G>C		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000648852.1	n.276+4004G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15375 AN: 152110 Hom.: 1099 Cov.: 33

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.101 AC: 15373 AN: 152228 Hom.: 1099 Cov.: 33 AF XY: 0.101 AC XY: 7511 AN XY: 74430

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.129 Hom.: 187

Bravo AF: 0.0876

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873211; hg19: chr9-117735945;