chr9-115217131-A-G

Position:

• chr9-115217131-A-G

Variant summary

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

The NR_163556.1(DELEC1):​n.52-16045A>G 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 0.136 in 152,120 control chromosomes in the GnomAD database, including 1,553 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 0.14 (1553 hom., cov: 32)
• Consequence: DELEC1 NR_163556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DELEC1	NR_163556.1	n.52-16045A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DELEC1	ENST00000374016.5	n.52-16045A>G		intron_variant, non_coding_transcript_variant		1
DELEC1	ENST00000484171.2	n.146+7056A>G		intron_variant, non_coding_transcript_variant		1
DELEC1	ENST00000649121.1	n.659-16045A>G		intron_variant, non_coding_transcript_variant
DELEC1	ENST00000647970.1	n.138+7056A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20632 AN: 152002 Hom.: 1555 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.136 AC: 20639 AN: 152120 Hom.: 1553 Cov.: 32 AF XY: 0.134 AC XY: 9941 AN XY: 74352

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.168

Alfa AF: 0.122 Hom.: 1604

Bravo AF: 0.141

Asia WGS AF: 0.117 AC: 404 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.55

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: rs10817727; hg19: chr9-117979410;