9-115386411-T-C

Variant names:

• chr9-115386411-T-C
• rs7859920
• ENST00000374016.5:n.532+9696T>C

Variant summary

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

The ENST00000374016.5(DELEC1):​n.532+9696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,074 control chromosomes in the GnomAD database, including 24,391 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 (24391 hom., cov: 33)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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.532+9696T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000374016.5	TSL:1	n.532+9696T>C		intron	N/A
	ENSG00000228714	ENST00000646338.1		n.276-60977A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85487 AN: 151956 Hom.: 24365 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.563 AC: 85564 AN: 152074 Hom.: 24391 Cov.: 33 AF XY: 0.566 AC XY: 42083 AN XY: 74338

African (AFR) AF: 0.677 AC: 28070 AN: 41486

American (AMR) AF: 0.528 AC: 8068 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2349 AN: 5158

South Asian (SAS) AF: 0.593 AC: 2861 AN: 4822

European-Finnish (FIN) AF: 0.584 AC: 6174 AN: 10576

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34461 AN: 67978

Other (OTH) AF: 0.553 AC: 1166 AN: 2110

Alfa AF: 0.523 Hom.: 81389

Bravo AF: 0.559

Asia WGS AF: 0.536 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.49
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: rs7859920; hg19: chr9-118148690;