Genetic Variant SCAMP2:c.*730A>G (chr15-74844353-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_005697.5(SCAMP2):c.*730A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,092 control chromosomes in the GnomAD database, including 12,636 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 0.35 ( 12622 hom., cov: 31)

Exomes 𝑓: 0.48 ( 14 hom. )

Consequence

SCAMP2
NM_005697.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

Publications

19 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAMP2	NM_005697.5 link	c.*730A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000268099.13	NP_005688.2
SCAMP2	NM_001320778.2 link	c.*730A>G		3_prime_UTR_variant	Exon 10 of 10		NP_001307707.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
SCAMP2	ENST00000268099.13 link	c.*730A>G	3_prime_UTR_variant	Exon 9 of 9	1	NM_005697.5	ENSP00000268099.9
SCAMP2	ENST00000563663.5 link	n.*924A>G	non_coding_transcript_exon_variant	Exon 4 of 4	5		ENSP00000455963.1
SCAMP2	ENST00000566480.5 link	c.*1018A>G	3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000455377.1
SCAMP2	ENST00000563663.5 link	n.*924A>G	3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000455963.1

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53793

AN:

151842

Hom.:

12627

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0973

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.0692

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.379

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.348

GnomAD4 exome

AF:

0.477

AC:

AN:

132

Hom.:

Cov.:

AF XY:

0.480

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

108

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.354

AC:

53784

AN:

151960

Hom.:

12622

Cov.:

AF XY:

0.343

AC XY:

25466

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.0971

AC:

4026

AN:

41462

American (AMR)

AF:

0.286

AC:

4369

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.422

AC:

1461

AN:

3466

East Asian (EAS)

AF:

0.0690

AC:

357

AN:

5176

South Asian (SAS)

AF:

0.138

AC:

664

AN:

4814

European-Finnish (FIN)

AF:

0.462

AC:

4866

AN:

10540

Middle Eastern (MID)

AF:

0.387

AC:

113

AN:

292

European-Non Finnish (NFE)

AF:

0.542

AC:

36822

AN:

67912

Other (OTH)

AF:

0.348

AC:

736

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1473

2946

4420

5893

7366

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.329

Hom.:

5053

Bravo

AF:

0.337

Asia WGS

AF:

0.103

AC:

364

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.80

(source)

DANN

Benign

0.54

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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