rs1250288

Variant names:

• chr9-115245153-C-T
• rs1250288
• ENST00000374016.5:n.212+11817C>T

Variant summary

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

The ENST00000374016.5(DELEC1):​n.212+11817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,998 control chromosomes in the GnomAD database, including 16,160 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 0.45 (16160 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2	n.212+11817C>T		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.212+11817C>T		intron_variant	Intron 2 of 7	1
DELEC1	ENST00000484171.2	n.307+11817C>T		intron_variant	Intron 2 of 4	1
DELEC1	ENST00000647970.1	n.299+11817C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68484 AN: 151880 Hom.: 16143 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.451 AC: 68539 AN: 151998 Hom.: 16160 Cov.: 32 AF XY: 0.457 AC XY: 33922 AN XY: 74282

African (AFR) AF: 0.502 AC: 20813 AN: 41444

American (AMR) AF: 0.537 AC: 8197 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3884 AN: 5162

South Asian (SAS) AF: 0.439 AC: 2116 AN: 4818

European-Finnish (FIN) AF: 0.392 AC: 4136 AN: 10560

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26272 AN: 67968

Other (OTH) AF: 0.451 AC: 950 AN: 2108

Alfa AF: 0.435 Hom.: 2471

Bravo AF: 0.470

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.49
PhyloP100		-0.58
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: rs1250288; hg19: chr9-118007432;