rs2071520

Variant names:

• chr9-115118513-A-G
• rs2071520
• ENST00000825497.1:n.518T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-115118513-A-G
• chr9-115118513-A-T

Variant summary

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

The ENST00000825497.1(ENSG00000307377):​n.518T>C 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 0.294 in 151,678 control chromosomes in the GnomAD database, including 6,827 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 0.29 (6827 hom., cov: 31)
• Consequence: ENSG00000307377 ENST00000825497.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 7 publications found

Genes affected

ENSG00000307377 (HGNC:):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902255	XR_007061746.1	n.188-2443A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307377	ENST00000825497.1	n.518T>C		non_coding_transcript_exon_variant	Exon 1 of 1
DELEC1	ENST00000648852.1	n.481-2443A>G		intron_variant	Intron 5 of 5
DELEC1	ENST00000649121.1	n.323-23141A>G		intron_variant	Intron 3 of 6
DELEC1	ENST00000825162.1	n.278-2443A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44584 AN: 151560 Hom.: 6820 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.294 AC: 44613 AN: 151678 Hom.: 6827 Cov.: 31 AF XY: 0.297 AC XY: 21992 AN XY: 74076

African (AFR) AF: 0.227 AC: 9394 AN: 41336

American (AMR) AF: 0.251 AC: 3816 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1494 AN: 5114

South Asian (SAS) AF: 0.331 AC: 1586 AN: 4798

European-Finnish (FIN) AF: 0.403 AC: 4232 AN: 10502

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22217 AN: 67922

Other (OTH) AF: 0.284 AC: 600 AN: 2112

Alfa AF: 0.306 Hom.: 19378

Bravo AF: 0.279

Asia WGS AF: 0.318 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		-0.18
PromoterAI		-0.026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2071520; hg19: chr9-117880792; COSMIC: COSV60782806;