Genetic Variant DELEC1:n.698C>T (chr9-115401284-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000374016.5(DELEC1):n.698C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,609,608 control chromosomes in the GnomAD database, including 338,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.71 ( 39266 hom., cov: 32)

Exomes 𝑓: 0.64 ( 298779 hom. )

Consequence

DELEC1
ENST00000374016.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.225

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]

DELEC1 links:

ENSG00000228714 (HGNC:):

ENSG00000228714 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.583662E-7).

BP6

Variant 9-115401284-C-T is Benign according to our data. Variant chr9-115401284-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.1 link	n.698C>T		non_coding_transcript_exon_variant	Exon 7 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DELEC1	ENST00000374016.5 link	n.698C>T	non_coding_transcript_exon_variant	Exon 7 of 8	1
DELEC1	ENST00000614246.1 link	n.179C>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000228714	ENST00000646338.1 link	n.276-75850G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.710

AC:

107802

AN:

151862

Hom.:

39220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.879

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.636

Gnomad ASJ

AF:

0.598

Gnomad EAS

AF:

0.844

Gnomad SAS

AF:

0.701

Gnomad FIN

AF:

0.692

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.671

GnomAD2 exomes

AF:

0.672

AC:

168576

AN:

250848

AF XY:

0.667

show subpopulations

Gnomad AFR exome

AF:

0.890

Gnomad AMR exome

AF:

0.614

Gnomad ASJ exome

AF:

0.601

Gnomad EAS exome

AF:

0.851

Gnomad FIN exome

AF:

0.693

Gnomad NFE exome

AF:

0.625

Gnomad OTH exome

AF:

0.646

GnomAD4 exome

AF:

0.637

AC:

928175

AN:

1457628

Hom.:

298779

Cov.:

AF XY:

0.637

AC XY:

462118

AN XY:

725330

show subpopulations

Gnomad4 AFR exome

AF:

0.887

AC:

29585

AN:

33346

Gnomad4 AMR exome

AF:

0.612

AC:

27328

AN:

44630

Gnomad4 ASJ exome

AF:

0.604

AC:

15739

AN:

26050

Gnomad4 EAS exome

AF:

0.875

AC:

34727

AN:

39682

Gnomad4 SAS exome

AF:

0.701

AC:

60402

AN:

86164

Gnomad4 FIN exome

AF:

0.690

AC:

36866

AN:

53396

Gnomad4 NFE exome

AF:

0.614

AC:

680676

AN:

1108408

Gnomad4 Remaining exome

AF:

0.650

AC:

39144

AN:

60204

Heterozygous variant carriers

15193

30386

45580

60773

75966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

18432

36864

55296

73728

92160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.710

AC:

107911

AN:

151980

Hom.:

39266

Cov.:

AF XY:

0.712

AC XY:

52877

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.879

AC:

0.87858

AN:

0.87858

Gnomad4 AMR

AF:

0.636

AC:

0.63625

AN:

0.63625

Gnomad4 ASJ

AF:

0.598

AC:

0.598039

AN:

0.598039

Gnomad4 EAS

AF:

0.844

AC:

0.843592

AN:

0.843592

Gnomad4 SAS

AF:

0.701

AC:

0.701202

AN:

0.701202

Gnomad4 FIN

AF:

0.692

AC:

0.691886

AN:

0.691886

Gnomad4 NFE

AF:

0.625

AC:

0.625431

AN:

0.625431

Gnomad4 OTH

AF:

0.674

AC:

0.673913

AN:

0.673913

Heterozygous variant carriers

1554

3108

4662

6216

7770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

826

1652

2478

3304

4130

<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:

0.651

Hom.:

111163

Bravo

AF:

0.708

TwinsUK

AF:

0.615

AC:

2280

ALSPAC

AF:

0.602

AC:

2321

ESP6500AA

AF:

0.876

AC:

3858

ESP6500EA

AF:

0.616

AC:

5294

ExAC

AF:

0.677

AC:

82251

Asia WGS

AF:

0.787

AC:

2737

AN:

3478

EpiCase

AF:

0.614

EpiControl

AF:

0.613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

3.0

DANN

Benign

0.36

DEOGEN2

Benign

0.0078

T;.

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.00026

LIST_S2

Benign

0.31

T;.

MetaRNN

Benign

8.6e-7

T;T

MetaSVM

Benign

-1.0

Sift4G

Benign

1.0

.;T

Polyphen

0.0

B;.

ClinPred

0.00046

GERP RS

-1.6

Varity_R

0.022

gMVP

0.00055

Mutation Taster

=100/0

polymorphism (auto)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over