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GeneBe

1-155256413-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_005698.4(SCAMP3):c.904T>G(p.Ser302Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SCAMP3
NM_005698.4 missense

Scores

3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.10
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.28713685).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCAMP3NM_005698.4 linkuse as main transcriptc.904T>G p.Ser302Ala missense_variant 9/9 ENST00000302631.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCAMP3ENST00000302631.8 linkuse as main transcriptc.904T>G p.Ser302Ala missense_variant 9/91 NM_005698.4 P1O14828-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 16, 2021The c.904T>G (p.S302A) alteration is located in exon 9 (coding exon 9) of the SCAMP3 gene. This alteration results from a T to G substitution at nucleotide position 904, causing the serine (S) at amino acid position 302 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.42
Cadd
Benign
23
Dann
Uncertain
1.0
DEOGEN2
Benign
0.019
T;.
Eigen
Benign
0.014
Eigen_PC
Benign
0.10
FATHMM_MKL
Uncertain
0.92
D
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.29
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
-1.5
N;N
REVEL
Benign
0.082
Sift
Benign
0.22
T;T
Sift4G
Benign
0.52
T;T
Polyphen
1.0
D;B
Vest4
0.52
MutPred
0.52
Loss of disorder (P = 0.0975);.;
MVP
0.28
MPC
0.83
ClinPred
0.79
D
GERP RS
4.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.15
gMVP
0.57

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-155226204; API