9-114979060-G-A

Variant names:

• chr9-114979060-G-A
• rs11787779
• ENST00000648852.1:n.276+9399G>A

Variant summary

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

The ENST00000648852.1(DELEC1):​n.276+9399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,102 control chromosomes in the GnomAD database, including 1,936 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 0.14 (1936 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 4 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]

ENSG00000299819 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.269 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	ENST00000648852.1	n.276+9399G>A		intron_variant	Intron 3 of 5
DELEC1	ENST00000649121.1	n.78+9399G>A		intron_variant	Intron 1 of 6
ENSG00000299819	ENST00000766667.1	n.87+20993C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21028 AN: 151982 Hom.: 1925 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.138 AC: 21043 AN: 152102 Hom.: 1936 Cov.: 32 AF XY: 0.140 AC XY: 10424 AN XY: 74342

African (AFR) AF: 0.0347 AC: 1440 AN: 41514

American (AMR) AF: 0.241 AC: 3675 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1454 AN: 5166

South Asian (SAS) AF: 0.119 AC: 574 AN: 4822

European-Finnish (FIN) AF: 0.186 AC: 1966 AN: 10576

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11403 AN: 67968

Other (OTH) AF: 0.113 AC: 239 AN: 2116

Alfa AF: 0.155 Hom.: 6081

Bravo AF: 0.140

Asia WGS AF: 0.208 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.48
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs11787779; hg19: chr9-117741340;