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GeneBe

15-74854632-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005697.5(SCAMP2):c.75G>C(p.Gln25His) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SCAMP2
NM_005697.5 missense

Scores

4
6
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.65
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCAMP2NM_005697.5 linkuse as main transcriptc.75G>C p.Gln25His missense_variant 2/9 ENST00000268099.13
SCAMP2NM_001320778.2 linkuse as main transcriptc.75G>C p.Gln25His missense_variant 2/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCAMP2ENST00000268099.13 linkuse as main transcriptc.75G>C p.Gln25His missense_variant 2/91 NM_005697.5 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000417
AC:
1
AN:
239746
Hom.:
0
AF XY:
0.00000768
AC XY:
1
AN XY:
130200
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000557
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1457062
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
724356
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

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 GeneticsMay 03, 2023The c.75G>C (p.Q25H) alteration is located in exon 2 (coding exon 2) of the SCAMP2 gene. This alteration results from a G to C substitution at nucleotide position 75, causing the glutamine (Q) at amino acid position 25 to be replaced by a histidine (H). 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
0.29
BayesDel_addAF
Benign
-0.060
T
BayesDel_noAF
Benign
-0.15
Cadd
Uncertain
25
Dann
Uncertain
1.0
DEOGEN2
Benign
0.17
T;T
Eigen
Pathogenic
0.84
Eigen_PC
Pathogenic
0.82
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.83
T;D
M_CAP
Benign
0.023
T
MetaRNN
Uncertain
0.64
D;D
MetaSVM
Benign
-0.97
T
MutationAssessor
Pathogenic
3.0
M;.
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.74
T
PROVEAN
Uncertain
-2.9
D;D
REVEL
Benign
0.25
Sift
Uncertain
0.0010
D;D
Sift4G
Uncertain
0.0050
D;.
Polyphen
1.0
D;.
Vest4
0.72
MutPred
0.39
Gain of catalytic residue at Q25 (P = 0.0986);Gain of catalytic residue at Q25 (P = 0.0986);
MVP
0.79
MPC
0.62
ClinPred
0.95
D
GERP RS
5.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.52
gMVP
0.60

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1294432915; hg19: chr15-75146973; API