rs2071520

chr9-115118513-A-Gchr9-115118513-A-T

Variant summary

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

The ENST00000649121.1(DELEC1):n.323-23141A>G 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 0.294 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: DELEC1 ENST00000649121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

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]

LOC124902255 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902255	XR_007061746.1	n.188-2443A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000649121.1	n.323-23141A>G		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000648852.1	n.481-2443A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.284

Alfa AF: 0.309 Hom.: 11718

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

Splicing

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

Publications

LitVar

Other links and lift over

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