dbSNP rs3750505: DELEC1:n.902G>A (chr9-115402295-G-A) – 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.902G>A 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 0.13 in 925,834 control chromosomes in the GnomAD database, including 9,243 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 0.16 ( 2152 hom., cov: 31)

Exomes 𝑓: 0.12 ( 7091 hom. )

Consequence

DELEC1
ENST00000374016.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.672

Publications

7 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:

Genome browser will be placed here

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 = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DELEC1	NR_163556.2 link	n.902G>A		non_coding_transcript_exon_variant	Exon 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5 link	n.902G>A		non_coding_transcript_exon_variant	Exon 8 of 8	1
ENSG00000228714	ENST00000646338.1 link	n.276-76861C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23806

AN:

151792

Hom.:

2151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.125

AC:

96555

AN:

773924

Hom.:

7091

Cov.:

AF XY:

0.122

AC XY:

48158

AN XY:

394416

show subpopulations

African (AFR)

AF:

0.225

AC:

3969

AN:

17632

American (AMR)

AF:

0.148

AC:

2618

AN:

17714

Ashkenazi Jewish (ASJ)

AF:

0.0612

AC:

955

AN:

15602

East Asian (EAS)

AF:

0.296

AC:

9541

AN:

32186

South Asian (SAS)

AF:

0.0868

AC:

4260

AN:

49088

European-Finnish (FIN)

AF:

0.176

AC:

7815

AN:

44296

Middle Eastern (MID)

AF:

0.0346

AC:

146

AN:

4224

European-Non Finnish (NFE)

AF:

0.113

AC:

62659

AN:

556950

Other (OTH)

AF:

0.127

AC:

4592

AN:

36232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

4011

8021

12032

16042

20053

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1838

3676

5514

7352

9190

<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:

0.157

AC:

23828

AN:

151910

Hom.:

2152

Cov.:

AF XY:

0.159

AC XY:

11813

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.224

AC:

9288

AN:

41408

American (AMR)

AF:

0.142

AC:

2164

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0600

AC:

208

AN:

3468

East Asian (EAS)

AF:

0.318

AC:

1632

AN:

5140

South Asian (SAS)

AF:

0.106

AC:

508

AN:

4806

European-Finnish (FIN)

AF:

0.177

AC:

1871

AN:

10544

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7790

AN:

67956

Other (OTH)

AF:

0.131

AC:

277

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

990

1980

2969

3959

4949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.131

Hom.:

353

Bravo

AF:

0.158

Asia WGS

AF:

0.216

AC:

750

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

(source)

DANN

Benign

0.54

PhyloP100

-0.67

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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