Genetic Variant ENST00000374016.5:n.698C>T (chr9-115401284-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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

Publications

31 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]

DELEC1 links:

ENSG00000228714 (HGNC:):

ENSG00000228714 links:

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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 (MetaRNN=8.583662E-7).

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_163556.2 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

African (AFR)

AF:

0.887

AC:

29585

AN:

33346

American (AMR)

AF:

0.612

AC:

27328

AN:

44630

Ashkenazi Jewish (ASJ)

AF:

0.604

AC:

15739

AN:

26050

East Asian (EAS)

AF:

0.875

AC:

34727

AN:

39682

South Asian (SAS)

AF:

0.701

AC:

60402

AN:

86164

European-Finnish (FIN)

AF:

0.690

AC:

36866

AN:

53396

Middle Eastern (MID)

AF:

0.645

AC:

3708

AN:

5748

European-Non Finnish (NFE)

AF:

0.614

AC:

680676

AN:

1108408

Other (OTH)

AF:

0.650

AC:

39144

AN:

60204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

15193

30386

45580

60773

75966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

African (AFR)

AF:

0.879

AC:

36447

AN:

41484

American (AMR)

AF:

0.636

AC:

9699

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.598

AC:

2074

AN:

3468

East Asian (EAS)

AF:

0.844

AC:

4331

AN:

5134

South Asian (SAS)

AF:

0.701

AC:

3384

AN:

4826

European-Finnish (FIN)

AF:

0.692

AC:

7316

AN:

10574

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.625

AC:

42488

AN:

67934

Other (OTH)

AF:

0.674

AC:

1426

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1554

3108

4662

6216

7770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

(source)

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

PhyloP100

0.23

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over