Genetic Variant SCAMP2:c.734+87C>T (chr15-74848513-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005697.5(SCAMP2):c.734+87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 829,814 control chromosomes in the GnomAD database, including 146,808 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 0.48 ( 21074 hom., cov: 31)

Exomes 𝑓: 0.59 ( 125734 hom. )

Consequence

SCAMP2
NM_005697.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

Publications

27 publications found

Variant links:

Genes affected

SCAMP2 (HGNC:10564): (secretory carrier membrane protein 2) This gene product belongs to the SCAMP family of proteins which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that the SCAMPs may function at the same site during vesicular transport rather than in separate pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

SCAMP2 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 (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAMP2	NM_005697.5 link	c.734+87C>T		intron_variant	Intron 7 of 8	ENST00000268099.13	NP_005688.2	O15127A0A140VK92
SCAMP2	NM_001320778.2 link	c.863+87C>T		intron_variant	Intron 8 of 9		NP_001307707.1	A8K769

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099.13 link	c.734+87C>T		intron_variant	Intron 7 of 8	1	NM_005697.5	ENSP00000268099.9		O15127

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73594

AN:

151886

Hom.:

21079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.604

Gnomad EAS

AF:

0.515

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.569

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.655

Gnomad OTH

AF:

0.510

GnomAD4 exome

AF:

0.595

AC:

402977

AN:

677810

Hom.:

125734

Cov.:

AF XY:

0.583

AC XY:

206237

AN XY:

353888

show subpopulations

African (AFR)

AF:

0.168

AC:

2817

AN:

16744

American (AMR)

AF:

0.479

AC:

13268

AN:

27722

Ashkenazi Jewish (ASJ)

AF:

0.618

AC:

10541

AN:

17054

East Asian (EAS)

AF:

0.492

AC:

16243

AN:

33010

South Asian (SAS)

AF:

0.302

AC:

16984

AN:

56174

European-Finnish (FIN)

AF:

0.578

AC:

27350

AN:

47318

Middle Eastern (MID)

AF:

0.567

AC:

1581

AN:

2788

European-Non Finnish (NFE)

AF:

0.665

AC:

294899

AN:

443498

Other (OTH)

AF:

0.576

AC:

19294

AN:

33502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

7292

14584

21875

29167

36459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4328

8656

12984

17312

21640

<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:

0.484

AC:

73595

AN:

152004

Hom.:

21074

Cov.:

AF XY:

0.477

AC XY:

35427

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.175

AC:

7276

AN:

41486

American (AMR)

AF:

0.511

AC:

7793

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.604

AC:

2097

AN:

3470

East Asian (EAS)

AF:

0.514

AC:

2648

AN:

5150

South Asian (SAS)

AF:

0.294

AC:

1415

AN:

4812

European-Finnish (FIN)

AF:

0.569

AC:

6006

AN:

10548

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.655

AC:

44506

AN:

67976

Other (OTH)

AF:

0.509

AC:

1074

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1632

3264

4895

6527

8159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<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:

0.592

Hom.:

35796

Bravo

AF:

0.476

Asia WGS

AF:

0.375

AC:

1308

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.7

(source)

DANN

Benign

0.40

PhyloP100

1.1

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