Genetic Variant ENST00000484171.2:n.979T>C (chr9-115330728-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000484171.2(DELEC1):n.979T>C 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 0.333 in 152,174 control chromosomes in the GnomAD database, including 8,534 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 0.33 ( 8532 hom., cov: 33)

Exomes 𝑓: 0.64 ( 2 hom. )

Consequence

DELEC1
ENST00000484171.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.418

Publications

1 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

new If you want to explore the variant's impact on the transcript ENST00000484171.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484171.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	NR_163556.2		n.458+24732T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
DELEC1	ENST00000484171.2	TSL:1	n.979T>C	non_coding_transcript_exon	Exon 5 of 5
DELEC1	ENST00000374016.5	TSL:1	n.458+24732T>C	intron	N/A
DELEC1	ENST00000807886.1		n.872T>C	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50698

AN:

152042

Hom.:

8523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.340

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.316

Gnomad OTH

AF:

0.333

GnomAD4 exome

AF:

0.643

AC:

AN:

Hom.:

Cov.:

AF XY:

0.643

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.583

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.333

AC:

50730

AN:

152160

Hom.:

8532

Cov.:

AF XY:

0.337

AC XY:

25050

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.330

AC:

13698

AN:

41492

American (AMR)

AF:

0.395

AC:

6034

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

1198

AN:

3472

East Asian (EAS)

AF:

0.340

AC:

1758

AN:

5164

South Asian (SAS)

AF:

0.382

AC:

1845

AN:

4828

European-Finnish (FIN)

AF:

0.340

AC:

3604

AN:

10592

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.316

AC:

21497

AN:

68008

Other (OTH)

AF:

0.333

AC:

704

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1809

3618

5427

7236

9045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.323

Hom.:

10595

Bravo

AF:

0.336

Asia WGS

AF:

0.359

AC:

1252

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.6

(source)

DANN

Benign

0.83

PhyloP100

0.42

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over