dbSNP rs12674766: ADAM7-AS1:n.355+2942G>A (chr8-24384219-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000518988.5(ADAM7-AS1):n.355+2942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 356,086 control chromosomes in the GnomAD database, including 27,744 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 ( 10147 hom., cov: 32)

Exomes 𝑓: 0.40 ( 17597 hom. )

Consequence

ADAM7-AS1
ENST00000518988.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.05

Publications

4 publications found

Variant links:

Genes affected

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

ADAM7-AS1 links:

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:

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAM7-AS1	NR_125808.1 link	n.501+2942G>A		intron_variant	Intron 3 of 5
ADAMDEC1	NM_014479.3 link	c.-286C>T		upstream_gene_variant		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.-286C>T		upstream_gene_variant		1	NM_014479.3	ENSP00000256412.4		O15204-1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51113

AN:

151830

Hom.:

10151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.185

Gnomad SAS

AF:

0.403

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.432

Gnomad OTH

AF:

0.350

GnomAD4 exome

AF:

0.402

AC:

82120

AN:

204136

Hom.:

17597

AF XY:

0.404

AC XY:

42301

AN XY:

104800

show subpopulations

African (AFR)

AF:

0.127

AC:

752

AN:

5910

American (AMR)

AF:

0.452

AC:

3088

AN:

6838

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

3533

AN:

7378

East Asian (EAS)

AF:

0.233

AC:

3739

AN:

16066

South Asian (SAS)

AF:

0.400

AC:

3299

AN:

8242

European-Finnish (FIN)

AF:

0.429

AC:

6663

AN:

15546

Middle Eastern (MID)

AF:

0.396

AC:

406

AN:

1024

European-Non Finnish (NFE)

AF:

0.428

AC:

55299

AN:

129318

Other (OTH)

AF:

0.387

AC:

5341

AN:

13814

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

2262

4524

6787

9049

11311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

236

472

708

944

1180

<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:

0.336

AC:

51105

AN:

151950

Hom.:

10147

Cov.:

AF XY:

0.338

AC XY:

25085

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.122

AC:

5071

AN:

41478

American (AMR)

AF:

0.426

AC:

6488

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.467

AC:

1621

AN:

3468

East Asian (EAS)

AF:

0.185

AC:

954

AN:

5152

South Asian (SAS)

AF:

0.402

AC:

1934

AN:

4810

European-Finnish (FIN)

AF:

0.431

AC:

4541

AN:

10544

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.432

AC:

29367

AN:

67936

Other (OTH)

AF:

0.346

AC:

730

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1589

3178

4766

6355

7944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.363

Hom.:

1737

Bravo

AF:

0.325

Asia WGS

AF:

0.309

AC:

1074

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.019

(source)

DANN

Benign

0.55

PhyloP100

-2.1

PromoterAI

0.015

Neutral

(source)

Splicing

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