rs2075533

Positions:

• chr9-114931351-G-A
• chr9-114931351-G-T

Variant summary

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

The ENST00000648852.1(DELEC1):​n.198+9753G>A 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 0.556 in 151,878 control chromosomes in the GnomAD database, including 25,685 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 0.56 (25685 hom., cov: 31)
• Consequence: DELEC1 ENST00000648852.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 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.198+9753G>A		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000649565.1	n.226-38233G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84383 AN: 151760 Hom.: 25625 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.556 AC: 84515 AN: 151878 Hom.: 25685 Cov.: 31 AF XY: 0.558 AC XY: 41451 AN XY: 74228

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.517

Alfa AF: 0.537 Hom.: 3828

Bravo AF: 0.582

Asia WGS AF: 0.508 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2075533; hg19: chr9-117693631;