rs3750505

Positions:

• chr9-115402295-G-A

Variant summary

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

The NR_163556.1(DELEC1):​n.902G>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 0.13 in 925,834 control chromosomes in the GnomAD database, including 9,243 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 0.16 (2152 hom., cov: 31)
  • Exomes 𝑓: 0.12 (7091 hom.)
• Consequence: DELEC1 NR_163556.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DELEC1	NR_163556.1	n.902G>A		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.902G>A		non_coding_transcript_exon_variant	8/8	1
	ENST00000646338.1	n.276-76861C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23806 AN: 151792 Hom.: 2151 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.125 AC: 96555 AN: 773924 Hom.: 7091 Cov.: 10 AF XY: 0.122 AC XY: 48158 AN XY: 394416

Gnomad4 AFR exome AF: 0.225

Gnomad4 AMR exome AF: 0.148

Gnomad4 ASJ exome AF: 0.0612

Gnomad4 EAS exome AF: 0.296

Gnomad4 SAS exome AF: 0.0868

Gnomad4 FIN exome AF: 0.176

Gnomad4 NFE exome AF: 0.113

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome AF: 0.157 AC: 23828 AN: 151910 Hom.: 2152 Cov.: 31 AF XY: 0.159 AC XY: 11813 AN XY: 74232

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.131

Alfa AF: 0.131 Hom.: 353

Bravo AF: 0.158

Asia WGS AF: 0.216 AC: 750 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	1.5
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3750505; hg19: chr9-118164574; COSMIC: COSV64980565; COSMIC: COSV64980565;