9-114931904-G-A

Variant names:

• chr9-114931904-G-A
• rs3181348
• ENST00000815338.1:n.2232G>A

Variant summary

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

The ENST00000815338.1(DELEC1):​n.2232G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,062 control chromosomes in the GnomAD database, including 25,663 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 0.56 (25663 hom., cov: 32)
• Consequence: DELEC1 ENST00000815338.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 20 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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	ENST00000815338.1	n.2232G>A		non_coding_transcript_exon_variant	Exon 3 of 3
DELEC1	ENST00000648852.1	n.198+10306G>A		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-37680G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84429 AN: 151942 Hom.: 25609 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.556 AC: 84554 AN: 152062 Hom.: 25663 Cov.: 32 AF XY: 0.558 AC XY: 41492 AN XY: 74340

African (AFR) AF: 0.797 AC: 33083 AN: 41506

American (AMR) AF: 0.636 AC: 9717 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2100 AN: 5164

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4818

European-Finnish (FIN) AF: 0.477 AC: 5041 AN: 10558

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29186 AN: 67950

Other (OTH) AF: 0.517 AC: 1089 AN: 2106

Alfa AF: 0.470 Hom.: 14232

Bravo AF: 0.582

Asia WGS AF: 0.507 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs3181348; hg19: chr9-117694184;