rs10982724

Positions:

• chr9-115395450-T-C
• chr9-115395450-T-G

Variant summary

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

The NR_163556.1(DELEC1):​n.533-4909T>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 0.172 in 151,764 control chromosomes in the GnomAD database, including 2,700 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 0.17 (2700 hom., cov: 32)
• Consequence: DELEC1 NR_163556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DELEC1	NR_163556.1	n.533-4909T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.533-4909T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000646338.1	n.276-70016A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26073 AN: 151646 Hom.: 2696 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0595

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.172 AC: 26104 AN: 151764 Hom.: 2700 Cov.: 32 AF XY: 0.174 AC XY: 12897 AN XY: 74186

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0595

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.144

Alfa AF: 0.115 Hom.: 2468

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.42

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: rs10982724; hg19: chr9-118157729;