rs7850103

chr9-115375556-A-Cchr9-115375556-A-Gchr9-115375556-A-T

Variant summary

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

The NR_163556.1(DELEC1):n.459-1086A>C variant causes a intron, non coding transcript 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 NR_163556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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=-0.96).
• 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/exons	MANE	UniProt
DELEC1	NR_163556.1	n.459-1086A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000374016.5	n.459-1086A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000646338.1	n.276-50122T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.691

Alfa AF: 0.638 Hom.: 52309

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

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: rs7850103; hg19: chr9-118137835; COSMIC: COSV64982393;