rs2075533

Variant names:

• chr9-114931351-G-A
• rs2075533
• ENST00000815338.1:n.1679G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-114931351-G-A
• chr9-114931351-G-T

Variant summary

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

The ENST00000815338.1(DELEC1):​n.1679G>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 151,878 control chromosomes in the GnomAD database, including 25,685 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 (25685 hom., cov: 31)
• Consequence: DELEC1 ENST00000815338.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 18 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 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.1679G>A		non_coding_transcript_exon_variant	Exon 3 of 3
DELEC1	ENST00000648852.1	n.198+9753G>A		intron_variant	Intron 2 of 5
DELEC1	ENST00000649565.1	n.226-38233G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84383 AN: 151760 Hom.: 25625 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.435

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: 84515 AN: 151878 Hom.: 25685 Cov.: 31 AF XY: 0.558 AC XY: 41451 AN XY: 74228

African (AFR) AF: 0.799 AC: 33102 AN: 41430

American (AMR) AF: 0.635 AC: 9691 AN: 15252

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

East Asian (EAS) AF: 0.405 AC: 2092 AN: 5160

South Asian (SAS) AF: 0.434 AC: 2092 AN: 4820

European-Finnish (FIN) AF: 0.477 AC: 5028 AN: 10534

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

European-Non Finnish (NFE) AF: 0.430 AC: 29171 AN: 67896

Other (OTH) AF: 0.517 AC: 1092 AN: 2112

Alfa AF: 0.519 Hom.: 7344

Bravo AF: 0.582

Asia WGS AF: 0.508 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2075533; hg19: chr9-117693631;