Genetic Variant NM_014479.3:c.846C>T (chr8-24398957-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014479.3(ADAMDEC1):c.846C>T(p.Ser282Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 1,613,164 control chromosomes in the GnomAD database, including 142,531 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 0.34 ( 10219 hom., cov: 31)

Exomes 𝑓: 0.42 ( 132312 hom. )

Consequence

ADAMDEC1
NM_014479.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22

Publications

17 publications found

Variant links:

Genes affected

ADAMDEC1 (HGNC:16299): (ADAM like decysin 1) This encoded protein is thought to be a secreted protein belonging to the disintegrin metalloproteinase family. Its expression is upregulated during dendritic cells maturation. This protein may play an important role in dendritic cell function and their interactions with germinal center T cells. [provided by RefSeq, Jul 2008]

ADAMDEC1 links:

ADAM7-AS1 (HGNC:56152): (ADAM7, ADAMDEC1 and ADAM28 antisense RNA 1)

ADAM7-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-2.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3 link	c.846C>T	p.Ser282Ser	synonymous_variant	Exon 9 of 14	ENST00000256412.8	NP_055294.1	O15204-1B7Z6V5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMDEC1	ENST00000256412.8 link	c.846C>T	p.Ser282Ser	synonymous_variant	Exon 9 of 14	1	NM_014479.3	ENSP00000256412.4		O15204-1

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

51830

AN:

151768

Hom.:

10223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.494

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.352

GnomAD2 exomes

AF:

0.400

AC:

100264

AN:

250552

AF XY:

0.406

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.466

Gnomad ASJ exome

AF:

0.505

Gnomad EAS exome

AF:

0.191

Gnomad FIN exome

AF:

0.425

Gnomad NFE exome

AF:

0.429

Gnomad OTH exome

AF:

0.423

GnomAD4 exome

AF:

0.420

AC:

614149

AN:

1461278

Hom.:

132312

Cov.:

AF XY:

0.422

AC XY:

306842

AN XY:

726968

show subpopulations

African (AFR)

AF:

0.131

AC:

4399

AN:

33454

American (AMR)

AF:

0.464

AC:

20723

AN:

44650

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

13142

AN:

26126

East Asian (EAS)

AF:

0.224

AC:

8889

AN:

39618

South Asian (SAS)

AF:

0.424

AC:

36542

AN:

86196

European-Finnish (FIN)

AF:

0.423

AC:

22609

AN:

53398

Middle Eastern (MID)

AF:

0.382

AC:

2204

AN:

5764

European-Non Finnish (NFE)

AF:

0.433

AC:

481405

AN:

1111700

Other (OTH)

AF:

0.401

AC:

24236

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

18925

37849

56774

75698

94623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14568

29136

43704

58272

72840

<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:

0.341

AC:

51823

AN:

151886

Hom.:

10219

Cov.:

AF XY:

0.343

AC XY:

25423

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.143

AC:

5915

AN:

41460

American (AMR)

AF:

0.426

AC:

6493

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.494

AC:

1714

AN:

3472

East Asian (EAS)

AF:

0.187

AC:

964

AN:

5160

South Asian (SAS)

AF:

0.404

AC:

1943

AN:

4812

European-Finnish (FIN)

AF:

0.421

AC:

4425

AN:

10516

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29236

AN:

67922

Other (OTH)

AF:

0.347

AC:

733

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1645

3291

4936

6582

8227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<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:

0.381

Hom.:

8577

Bravo

AF:

0.331

Asia WGS

AF:

0.308

AC:

1072

AN:

3478

EpiCase

AF:

0.418

EpiControl

AF:

0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.32

(source)

DANN

Benign

0.50

PhyloP100

-2.2

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