rs7850103

Variant names:

• chr9-115375556-A-C
• rs7850103
• ENST00000374016.5:n.459-1086A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-115375556-A-C
• chr9-115375556-A-G
• chr9-115375556-A-T

Variant summary

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

The ENST00000374016.5(DELEC1):​n.459-1086A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,130 control chromosomes in the GnomAD database, including 40,568 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 0.72 (40568 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• 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]

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 (AFR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2	n.459-1086A>C		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.459-1086A>C		intron_variant	Intron 4 of 7	1
ENSG00000228714	ENST00000646338.1	n.276-50122T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109707 AN: 152012 Hom.: 40522 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.722 AC: 109815 AN: 152130 Hom.: 40568 Cov.: 32 AF XY: 0.727 AC XY: 54105 AN XY: 74378

African (AFR) AF: 0.881 AC: 36552 AN: 41504

American (AMR) AF: 0.670 AC: 10250 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2071 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4504 AN: 5176

South Asian (SAS) AF: 0.732 AC: 3528 AN: 4820

European-Finnish (FIN) AF: 0.757 AC: 8015 AN: 10584

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42664 AN: 67968

Other (OTH) AF: 0.691 AC: 1457 AN: 2110

Alfa AF: 0.653 Hom.: 127916

Bravo AF: 0.718

Asia WGS AF: 0.811 AC: 2819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-1.6
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: rs7850103; hg19: chr9-118137835; COSMIC: COSV64982393;