chr9-115141569-T-C

Position:

• chr9-115141569-T-C

Variant summary

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

The ENST00000649121.1(DELEC1):​n.323-85T>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 0.299 in 151,962 control chromosomes in the GnomAD database, including 6,938 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 0.30 (6938 hom., cov: 31)
• Consequence: DELEC1 ENST00000649121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932

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 (EAS) allele frequency at 95% confidence interval = 0.483 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	ENST00000649121.1	n.323-85T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45467 AN: 151844 Hom.: 6932 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.299 AC: 45479 AN: 151962 Hom.: 6938 Cov.: 31 AF XY: 0.299 AC XY: 22215 AN XY: 74258

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.298

Alfa AF: 0.306 Hom.: 1220

Bravo AF: 0.299

Asia WGS AF: 0.387 AC: 1346 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	7.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2012775; hg19: chr9-117903848;