rs12006094

chr9-115009031-T-C

Variant summary

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

The ENST00000649121.1(DELEC1):n.78+39370T>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 0.157 in 152,078 control chromosomes in the GnomAD database, including 2,048 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 0.16 (2048 hom., cov: 31)
• Consequence: DELEC1 ENST00000649121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 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+39370T>C		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000648852.1	n.276+39370T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23868 AN: 151960 Hom.: 2047 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0263

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.157 AC: 23868 AN: 152078 Hom.: 2048 Cov.: 31 AF XY: 0.152 AC XY: 11285 AN XY: 74352

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.127

Alfa AF: 0.177 Hom.: 3377

Bravo AF: 0.149

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.74
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12006094; hg19: chr9-117771310;