rs12380804

Positions:

• chr9-115249771-G-A

Variant summary

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

The NR_163556.1(DELEC1):​n.212+16435G>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 0.0409 in 152,208 control chromosomes in the GnomAD database, including 169 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 0.041 (169 hom., cov: 32)
• Consequence: DELEC1 NR_163556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

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 (AMR) allele frequency at 95% confidence interval = 0.0552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DELEC1	NR_163556.1	n.212+16435G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.212+16435G>A		intron_variant, non_coding_transcript_variant		1
DELEC1	ENST00000484171.2	n.307+16435G>A		intron_variant, non_coding_transcript_variant		1
DELEC1	ENST00000647970.1	n.299+16435G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6229 AN: 152092 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0409 AC: 6226 AN: 152208 Hom.: 169 Cov.: 32 AF XY: 0.0406 AC XY: 3024 AN XY: 74406

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0513 Hom.: 123

Bravo AF: 0.0403

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.49

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: rs12380804; hg19: chr9-118012050;