rs7007084

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014479.3(ADAMDEC1):c.362T>C(p.Met121Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00489 in 1,607,606 control chromosomes in the GnomAD database, including 340 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.026 ( 164 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 176 hom. )

Consequence

ADAMDEC1
NM_014479.3 missense, splice_region

Scores

Splicing: ADA: 0.00001287

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.361

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00237903).

BP6

Variant 8-24394146-T-C is Benign according to our data. Variant chr8-24394146-T-C is described in ClinVar as Benign. ClinVar VariationId is 781121.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.088 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	HGVSp	Effect	Exon Rank	Protein	UniProt
ADAMDEC1	NM_014479.3	MANE Select	c.362T>C	p.Met121Thr	missense splice_region	Exon 4 of 14	NP_055294.1	O15204-1
ADAMDEC1	NM_001145271.2		c.125T>C	p.Met42Thr	missense splice_region	Exon 5 of 15	NP_001138743.1	O15204-2
ADAMDEC1	NM_001145272.2		c.125T>C	p.Met42Thr	missense splice_region	Exon 3 of 13	NP_001138744.1	O15204-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ADAMDEC1	ENST00000256412.8	TSL:1 MANE Select	c.362T>C	p.Met121Thr	missense splice_region	Exon 4 of 14	ENSP00000256412.4	O15204-1
ADAMDEC1	ENST00000893450.1		c.362T>C	p.Met121Thr	missense splice_region	Exon 4 of 13	ENSP00000563509.1
ADAMDEC1	ENST00000522298.1	TSL:2	c.125T>C	p.Met42Thr	missense splice_region	Exon 3 of 13	ENSP00000428993.1	O15204-2

Frequencies

GnomAD3 genomes

AF:

0.0257

AC:

3914

AN:

152140

Hom.:

162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0902

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00792

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000309

Gnomad OTH

AF:

0.0153

GnomAD2 exomes

AF:

0.00682

AC:

1710

AN:

250712

AF XY:

0.00505

show subpopulations

Gnomad AFR exome

AF:

0.0946

Gnomad AMR exome

AF:

0.00333

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000229

Gnomad OTH exome

AF:

0.00393

GnomAD4 exome

AF:

0.00270

AC:

3928

AN:

1455348

Hom.:

176

Cov.:

AF XY:

0.00226

AC XY:

1634

AN XY:

724360

show subpopulations

African (AFR)

AF:

0.0955

AC:

3180

AN:

33302

American (AMR)

AF:

0.00407

AC:

182

AN:

44702

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26096

East Asian (EAS)

AF:

0.00

AC:

AN:

39590

South Asian (SAS)

AF:

0.000314

AC:

AN:

86090

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53394

Middle Eastern (MID)

AF:

0.00296

AC:

AN:

5748

European-Non Finnish (NFE)

AF:

0.000139

AC:

154

AN:

1106276

Other (OTH)

AF:

0.00612

AC:

368

AN:

60150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

155

310

464

619

774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

204

306

408

510

<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:

0.0258

AC:

3932

AN:

152258

Hom.:

164

Cov.:

AF XY:

0.0249

AC XY:

1855

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0904

AC:

3756

AN:

41548

American (AMR)

AF:

0.00791

AC:

121

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.000207

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000309

AC:

AN:

68026

Other (OTH)

AF:

0.0151

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

177

353

530

706

883

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<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:

0.00953

Hom.:

173

Bravo

AF:

0.0293

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.0887

AC:

391

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00825

AC:

1001

Asia WGS

AF:

0.00491

AC:

AN:

3478

EpiCase

AF:

0.0000546

EpiControl

AF:

0.000357

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.75

CADD

Benign

6.2

(source)

DANN

Benign

0.50

DEOGEN2

Benign

0.0079

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.069

LIST_S2

Benign

0.42

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.20

PhyloP100

0.36

PrimateAI

Benign

0.34

PROVEAN

Benign

-1.8

REVEL

Benign

0.0080

Sift

Benign

0.17

Sift4G

Benign

0.36

Polyphen

0.0040

Vest4

0.19

MVP

0.15

MPC

0.062

ClinPred

0.0035

GERP RS

-0.31

Varity_R

0.089

gMVP

0.72

Mutation Taster

=90/10

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000013

dbscSNV1_RF

Benign

0.0020

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