rs998410

chr9-114860394-G-T

Variant summary

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

The ENST00000648852.1(DELEC1):n.49+9378G>T 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 0.0645 in 152,236 control chromosomes in the GnomAD database, including 793 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 0.064 (793 hom., cov: 33)
• Consequence: DELEC1 ENST00000648852.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.802

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

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 = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000648852.1	n.49+9378G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9793 AN: 152116 Hom.: 792 Cov.: 33

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0645 AC: 9817 AN: 152236 Hom.: 793 Cov.: 33 AF XY: 0.0728 AC XY: 5418 AN XY: 74442

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.0600

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0690 Hom.: 169

Bravo AF: 0.0713

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.7
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs998410; hg19: chr9-117622674;