dbSNP rs12334642: ADAMDEC1:c.-114T>C (chr8-24384391-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 NM_014479.3(ADAMDEC1):c.-114T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0309 in 834,136 control chromosomes in the GnomAD database, including 509 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 0.036 ( 129 hom., cov: 32)

Exomes 𝑓: 0.030 ( 380 hom. )

Consequence

ADAMDEC1
NM_014479.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

Publications

4 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014479.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADAMDEC1	NM_014479.3	MANE Select	c.-114T>C	5_prime_UTR	Exon 1 of 14	NP_055294.1	O15204-1
ADAM7-AS1	NR_125808.1		n.501+2770A>G	intron	N/A
ADAMDEC1	NM_001145271.2		c.-441T>C	upstream_gene	N/A	NP_001138743.1	O15204-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADAMDEC1	ENST00000256412.8	TSL:1 MANE Select	c.-114T>C	5_prime_UTR	Exon 1 of 14	ENSP00000256412.4	O15204-1
ADAM7-AS1	ENST00000518988.5	TSL:2	n.355+2770A>G	intron	N/A
ADAM7-AS1	ENST00000519689.1	TSL:4	n.606+2770A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0360

AC:

5470

AN:

152102

Hom.:

129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0499

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.0259

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.0689

Gnomad SAS

AF:

0.0394

Gnomad FIN

AF:

0.0364

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0266

Gnomad OTH

AF:

0.0368

GnomAD4 exome

AF:

0.0298

AC:

20341

AN:

681916

Hom.:

380

Cov.:

AF XY:

0.0299

AC XY:

10424

AN XY:

349200

show subpopulations

African (AFR)

AF:

0.0490

AC:

759

AN:

15484

American (AMR)

AF:

0.0254

AC:

433

AN:

17066

Ashkenazi Jewish (ASJ)

AF:

0.0260

AC:

386

AN:

14862

East Asian (EAS)

AF:

0.0798

AC:

2393

AN:

29982

South Asian (SAS)

AF:

0.0330

AC:

1613

AN:

48828

European-Finnish (FIN)

AF:

0.0385

AC:

1442

AN:

37460

Middle Eastern (MID)

AF:

0.0202

AC:

AN:

4018

European-Non Finnish (NFE)

AF:

0.0253

AC:

12181

AN:

480896

Other (OTH)

AF:

0.0316

AC:

1053

AN:

33320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

952

1904

2856

3808

4760

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

338

676

1014

1352

1690

<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:

0.0359

AC:

5467

AN:

152220

Hom.:

129

Cov.:

AF XY:

0.0359

AC XY:

2675

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0499

AC:

2072

AN:

41550

American (AMR)

AF:

0.0258

AC:

395

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0346

AC:

120

AN:

3470

East Asian (EAS)

AF:

0.0683

AC:

353

AN:

5166

South Asian (SAS)

AF:

0.0392

AC:

189

AN:

4824

European-Finnish (FIN)

AF:

0.0364

AC:

386

AN:

10608

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0266

AC:

1807

AN:

67992

Other (OTH)

AF:

0.0364

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

278

557

835

1114

1392

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0299

Hom.:

110

Bravo

AF:

0.0355

Asia WGS

AF:

0.0590

AC:

205

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.3

(source)

DANN

Benign

0.77

PhyloP100

-1.3

PromoterAI

-0.017

Neutral

(source)

Mutation Taster

=300/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over