9-115399318-A-C

Variant names:

• chr9-115399318-A-C
• rs10817762
• ENST00000374016.5:n.533-1041A>C

Variant summary

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

The ENST00000374016.5(DELEC1):​n.533-1041A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,982 control chromosomes in the GnomAD database, including 24,057 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 0.55 (24057 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 4 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]

ENSG00000228714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000374016.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	NR_163556.2		n.533-1041A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000374016.5	TSL:1	n.533-1041A>C		intron	N/A
	ENSG00000228714	ENST00000646338.1		n.276-73884T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83945 AN: 151864 Hom.: 24032 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.553 AC: 84024 AN: 151982 Hom.: 24057 Cov.: 32 AF XY: 0.553 AC XY: 41090 AN XY: 74280

African (AFR) AF: 0.685 AC: 28409 AN: 41462

American (AMR) AF: 0.490 AC: 7486 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4100 AN: 5148

South Asian (SAS) AF: 0.493 AC: 2371 AN: 4814

European-Finnish (FIN) AF: 0.535 AC: 5650 AN: 10562

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32878 AN: 67942

Other (OTH) AF: 0.519 AC: 1097 AN: 2114

Alfa AF: 0.509 Hom.: 39491

Bravo AF: 0.553

Asia WGS AF: 0.640 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10817762; hg19: chr9-118161597;