dbSNP rs2291578: ADAMDEC1:c.929+26G>T (chr8-24399066-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014479.3(ADAMDEC1):c.929+26G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,600,238 control chromosomes in the GnomAD database, including 17,031 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 0.12 ( 1404 hom., cov: 32)

Exomes 𝑓: 0.14 ( 15627 hom. )

Consequence

ADAMDEC1
NM_014479.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Publications

7 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3 link	c.929+26G>T		intron_variant	Intron 9 of 13	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.929+26G>T		intron_variant	Intron 9 of 13	1	NM_014479.3	ENSP00000256412.4		O15204-1

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17497

AN:

152042

Hom.:

1401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0368

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.0779

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.122

GnomAD2 exomes

AF:

0.151

AC:

36281

AN:

239652

AF XY:

0.154

show subpopulations

Gnomad AFR exome

AF:

0.0353

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.0730

Gnomad EAS exome

AF:

0.378

Gnomad FIN exome

AF:

0.147

Gnomad NFE exome

AF:

0.132

Gnomad OTH exome

AF:

0.130

GnomAD4 exome

AF:

0.138

AC:

199852

AN:

1448078

Hom.:

15627

Cov.:

AF XY:

0.139

AC XY:

99894

AN XY:

719178

show subpopulations

African (AFR)

AF:

0.0307

AC:

1017

AN:

33086

American (AMR)

AF:

0.149

AC:

6267

AN:

42078

Ashkenazi Jewish (ASJ)

AF:

0.0738

AC:

1880

AN:

25470

East Asian (EAS)

AF:

0.378

AC:

14877

AN:

39384

South Asian (SAS)

AF:

0.175

AC:

14711

AN:

84190

European-Finnish (FIN)

AF:

0.147

AC:

7838

AN:

53168

Middle Eastern (MID)

AF:

0.134

AC:

760

AN:

5688

European-Non Finnish (NFE)

AF:

0.131

AC:

144301

AN:

1105182

Other (OTH)

AF:

0.137

AC:

8201

AN:

59832

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

8153

16306

24458

32611

40764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5360

10720

16080

21440

26800

<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:

0.115

AC:

17521

AN:

152160

Hom.:

1404

Cov.:

AF XY:

0.120

AC XY:

8943

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.0367

AC:

1526

AN:

41548

American (AMR)

AF:

0.133

AC:

2031

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0779

AC:

270

AN:

3468

East Asian (EAS)

AF:

0.390

AC:

2010

AN:

5158

South Asian (SAS)

AF:

0.193

AC:

929

AN:

4818

European-Finnish (FIN)

AF:

0.141

AC:

1497

AN:

10584

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.131

AC:

8884

AN:

67982

Other (OTH)

AF:

0.124

AC:

261

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

760

1519

2279

3038

3798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.124

Hom.:

2280

Bravo

AF:

0.112

Asia WGS

AF:

0.248

AC:

861

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.20

(source)

DANN

Benign

0.43

PhyloP100

-0.60

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