Genetic Variant SCAMP2:c.226-571A>G (chr15-74852757-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.226-571A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,594 control chromosomes in the GnomAD database, including 33,941 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 0.66 ( 33823 hom., cov: 33)

Exomes 𝑓: 0.68 ( 118 hom. )

Consequence

SCAMP2
NM_005697.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.833

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:

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAMP2	NM_005697.5 link	c.226-571A>G		intron_variant	Intron 3 of 8	ENST00000268099.13	NP_005688.2	O15127A0A140VK92
SCAMP2	NM_001320778.2 link	c.355-571A>G		intron_variant	Intron 4 of 9		NP_001307707.1	A8K769

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAMP2	ENST00000268099.13 link	c.226-571A>G		intron_variant	Intron 3 of 8	1	NM_005697.5	ENSP00000268099.9		O15127

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

101011

AN:

152008

Hom.:

33789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.589

Gnomad AMI

AF:

0.747

Gnomad AMR

AF:

0.674

Gnomad ASJ

AF:

0.672

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.660

Gnomad FIN

AF:

0.672

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.701

Gnomad OTH

AF:

0.658

GnomAD4 exome

AF:

0.675

AC:

316

AN:

468

Hom.:

118

Cov.:

AF XY:

0.667

AC XY:

216

AN XY:

324

show subpopulations

African (AFR)

AF:

0.600

AC:

AN:

American (AMR)

AF:

0.833

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.571

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.683

AC:

276

AN:

404

Other (OTH)

AF:

0.692

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.665

AC:

101096

AN:

152126

Hom.:

33823

Cov.:

AF XY:

0.663

AC XY:

49267

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.590

AC:

24467

AN:

41504

American (AMR)

AF:

0.674

AC:

10313

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.672

AC:

2332

AN:

3470

East Asian (EAS)

AF:

0.724

AC:

3729

AN:

5152

South Asian (SAS)

AF:

0.659

AC:

3180

AN:

4824

European-Finnish (FIN)

AF:

0.672

AC:

7116

AN:

10582

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.701

AC:

47672

AN:

67980

Other (OTH)

AF:

0.660

AC:

1393

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1813

3625

5438

7250

9063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.672

Hom.:

5469

Bravo

AF:

0.665

Asia WGS

AF:

0.729

AC:

2536

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.1

(source)

DANN

Benign

0.50

PhyloP100

0.83

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