Genetic Variant SCAMP3:p.Gly126Gly (chr1-155260340-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005698.4(SCAMP3):c.378G>A(p.Gly126Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,611,504 control chromosomes in the GnomAD database, including 76,829 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 0.36 ( 11386 hom., cov: 32)

Exomes 𝑓: 0.28 ( 65443 hom. )

Consequence

SCAMP3
NM_005698.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Publications

42 publications found

Variant links:

Genes affected

SCAMP3 (HGNC:10565): (secretory carrier membrane protein 3) This gene encodes an integral membrane protein that belongs to the secretory carrier membrane protein family. The encoded protein functions as a carrier to the cell surface in post-golgi recycling pathways. This protein is also involved in protein trafficking in endosomal pathways. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

SCAMP3 links:

ENSG00000303088 (HGNC:):

ENSG00000303088 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-1.24 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAMP3	NM_005698.4 link	c.378G>A	p.Gly126Gly	synonymous_variant	Exon 4 of 9	ENST00000302631.8	NP_005689.2	O14828-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAMP3	ENST00000302631.8 link	c.378G>A	p.Gly126Gly	synonymous_variant	Exon 4 of 9	1	NM_005698.4	ENSP00000307275.3		O14828-1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54721

AN:

151892

Hom.:

11346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.702

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.339

GnomAD2 exomes

AF:

0.336

AC:

83946

AN:

250078

AF XY:

0.323

show subpopulations

Gnomad AFR exome

AF:

0.551

Gnomad AMR exome

AF:

0.408

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.705

Gnomad FIN exome

AF:

0.291

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.299

GnomAD4 exome

AF:

0.284

AC:

414222

AN:

1459492

Hom.:

65443

Cov.:

AF XY:

0.282

AC XY:

204808

AN XY:

726184

show subpopulations

African (AFR)

AF:

0.546

AC:

18268

AN:

33478

American (AMR)

AF:

0.402

AC:

17999

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.231

AC:

6044

AN:

26134

East Asian (EAS)

AF:

0.726

AC:

28801

AN:

39698

South Asian (SAS)

AF:

0.324

AC:

27942

AN:

86256

European-Finnish (FIN)

AF:

0.286

AC:

14621

AN:

51136

Middle Eastern (MID)

AF:

0.201

AC:

1161

AN:

5762

European-Non Finnish (NFE)

AF:

0.253

AC:

281126

AN:

1111932

Other (OTH)

AF:

0.302

AC:

18260

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

16359

32718

49077

65436

81795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10038

20076

30114

40152

50190

<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:

0.361

AC:

54812

AN:

152012

Hom.:

11386

Cov.:

AF XY:

0.362

AC XY:

26913

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.541

AC:

22431

AN:

41456

American (AMR)

AF:

0.334

AC:

5110

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

775

AN:

3472

East Asian (EAS)

AF:

0.702

AC:

3622

AN:

5162

South Asian (SAS)

AF:

0.338

AC:

1625

AN:

4814

European-Finnish (FIN)

AF:

0.296

AC:

3123

AN:

10548

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.254

AC:

17254

AN:

67960

Other (OTH)

AF:

0.335

AC:

704

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1671

3342

5013

6684

8355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<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:

0.298

Hom.:

27608

Bravo

AF:

0.377

Asia WGS

AF:

0.543

AC:

1889

AN:

3478

EpiCase

AF:

0.240

EpiControl

AF:

0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

3.4

(source)

DANN

Benign

0.81

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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