chr9-115386411-T-C

Position:

• chr9-115386411-T-C

Variant summary

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

The NR_163556.1(DELEC1):​n.532+9696T>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 0.563 in 152,074 control chromosomes in the GnomAD database, including 24,391 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 (24391 hom., cov: 33)
• Consequence: DELEC1 NR_163556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DELEC1	NR_163556.1	n.532+9696T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000374016.5	n.532+9696T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000646338.1	n.276-60977A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85487 AN: 151956 Hom.: 24365 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.563 AC: 85564 AN: 152074 Hom.: 24391 Cov.: 33 AF XY: 0.566 AC XY: 42083 AN XY: 74338

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.553

Alfa AF: 0.515 Hom.: 38471

Bravo AF: 0.559

Asia WGS AF: 0.536 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.50

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: rs7859920; hg19: chr9-118148690;