Genetic Variant NM_014479.3:c.1331A>G (chr8-24404013-A-G) – 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.1331A>G(p.Asn444Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 1,611,798 control chromosomes in the GnomAD database, including 144,173 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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 ( 10343 hom., cov: 32)

Exomes 𝑓: 0.42 ( 133830 hom. )

Consequence

ADAMDEC1
NM_014479.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.437

Publications

32 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.05593E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMDEC1	NM_014479.3 link	c.1331A>G	p.Asn444Ser	missense_variant	Exon 13 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.1331A>G	p.Asn444Ser	missense_variant	Exon 13 of 14	1	NM_014479.3	ENSP00000256412.4		O15204-1

Frequencies

GnomAD3 genomes

AF:

0.343

AC:

52117

AN:

151806

Hom.:

10348

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.357

GnomAD2 exomes

AF:

0.402

AC:

100789

AN:

250754

AF XY:

0.408

show subpopulations

Gnomad AFR exome

AF:

0.136

Gnomad AMR exome

AF:

0.468

Gnomad ASJ exome

AF:

0.506

Gnomad EAS exome

AF:

0.191

Gnomad FIN exome

AF:

0.426

Gnomad NFE exome

AF:

0.432

Gnomad OTH exome

AF:

0.425

GnomAD4 exome

AF:

0.423

AC:

616932

AN:

1459874

Hom.:

133830

Cov.:

AF XY:

0.424

AC XY:

308249

AN XY:

726278

show subpopulations

African (AFR)

AF:

0.132

AC:

4418

AN:

33458

American (AMR)

AF:

0.465

AC:

20780

AN:

44642

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

13162

AN:

26110

East Asian (EAS)

AF:

0.225

AC:

8902

AN:

39616

South Asian (SAS)

AF:

0.427

AC:

36798

AN:

86174

European-Finnish (FIN)

AF:

0.424

AC:

22649

AN:

53400

Middle Eastern (MID)

AF:

0.385

AC:

2218

AN:

5756

European-Non Finnish (NFE)

AF:

0.436

AC:

483630

AN:

1110400

Other (OTH)

AF:

0.404

AC:

24375

AN:

60318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

15818

31635

47453

63270

79088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.343

AC:

52109

AN:

151924

Hom.:

10343

Cov.:

AF XY:

0.344

AC XY:

25567

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.143

AC:

5947

AN:

41478

American (AMR)

AF:

0.427

AC:

6511

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.495

AC:

1719

AN:

3472

East Asian (EAS)

AF:

0.187

AC:

968

AN:

5164

South Asian (SAS)

AF:

0.407

AC:

1952

AN:

4800

European-Finnish (FIN)

AF:

0.421

AC:

4443

AN:

10544

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.433

AC:

29415

AN:

67924

Other (OTH)

AF:

0.352

AC:

743

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1617

3233

4850

6466

8083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.397

Hom.:

42803

Bravo

AF:

0.332

TwinsUK

AF:

0.440

AC:

1632

ALSPAC

AF:

0.426

AC:

1641

ESP6500AA

AF:

0.154

AC:

677

ESP6500EA

AF:

0.442

AC:

3804

ExAC

AF:

0.394

AC:

47775

Asia WGS

AF:

0.312

AC:

1085

AN:

3476

EpiCase

AF:

0.421

EpiControl

AF:

0.433

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.8

(source)

DANN

Benign

0.61

DEOGEN2

Benign

0.065

T;.

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.87

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.31

T;T

MetaRNN

Benign

0.00031

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.1

L;.

PhyloP100

0.44

PrimateAI

Benign

0.24

PROVEAN

Uncertain

-3.4

D;D

REVEL

Benign

0.064

Sift

Benign

0.25

T;T

Sift4G

Uncertain

0.051

T;D

Polyphen

0.93

P;.

Vest4

0.053

MPC

0.058

ClinPred

0.065

GERP RS

0.41

Varity_R

0.049

gMVP

0.46

Mutation Taster

=99/1

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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NM_014479.3:c.1331A>G

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