rs10817762

chr9-115399318-A-Cchr9-115399318-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.533-1041A>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 0.553 in 151,982 control chromosomes in the GnomAD database, including 24,057 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 0.55 (24057 hom., cov: 32)
• Consequence: DELEC1 NR_163556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

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 (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DELEC1	NR_163556.1	n.533-1041A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000374016.5	n.533-1041A>C		intron_variant, non_coding_transcript_variant		1
	ENST00000646338.1	n.276-73884T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83945 AN: 151864 Hom.: 24032 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.553 AC: 84024 AN: 151982 Hom.: 24057 Cov.: 32 AF XY: 0.553 AC XY: 41090 AN XY: 74280

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.519

Alfa AF: 0.491 Hom.: 25224

Bravo AF: 0.553

Asia WGS AF: 0.640 AC: 2227 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	1.1
Dann	Benign	0.56

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: rs10817762; hg19: chr9-118161597;