GeneBe

ENST00000648852.1:n.276+39572G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000648852.1(DELEC1):​n.276+39572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,162 control chromosomes in the GnomAD database, including 1,736 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 ( 1736 hom., cov: 33)

Consequence

DELEC1
ENST00000648852.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.29

Publications

2 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DELEC1ENST00000648852.1 linkn.276+39572G>A intron_variant Intron 3 of 5
DELEC1ENST00000649121.1 linkn.78+39572G>A intron_variant Intron 1 of 6

Frequencies

GnomAD3 genomes
AF:
0.143
AC:
21801
AN:
152044
Hom.:
1736
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0753
Gnomad AMI
AF:
0.337
Gnomad AMR
AF:
0.112
Gnomad ASJ
AF:
0.0715
Gnomad EAS
AF:
0.220
Gnomad SAS
AF:
0.149
Gnomad FIN
AF:
0.181
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.182
Gnomad OTH
AF:
0.117
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.143
AC:
21795
AN:
152162
Hom.:
1736
Cov.:
33
AF XY:
0.142
AC XY:
10563
AN XY:
74376
show subpopulations
African (AFR)
AF:
0.0751
AC:
3120
AN:
41544
American (AMR)
AF:
0.112
AC:
1709
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.0715
AC:
248
AN:
3468
East Asian (EAS)
AF:
0.220
AC:
1138
AN:
5170
South Asian (SAS)
AF:
0.148
AC:
716
AN:
4828
European-Finnish (FIN)
AF:
0.181
AC:
1913
AN:
10570
Middle Eastern (MID)
AF:
0.0952
AC:
28
AN:
294
European-Non Finnish (NFE)
AF:
0.182
AC:
12371
AN:
67976
Other (OTH)
AF:
0.116
AC:
245
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
940
1880
2821
3761
4701
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
246
492
738
984
1230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.170
Hom.:
1583
Bravo
AF:
0.134
Asia WGS
AF:
0.207
AC:
718
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.13
DANN
Benign
0.61
PhyloP100
-2.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs17239726; hg19: chr9-117771512; API