chr3-47418189-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_012235.4(SCAP):c.2392G>T(p.Val798Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SCAP
NM_012235.4 missense
NM_012235.4 missense
Scores
3
4
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.21
Publications
58 publications found
Genes affected
SCAP (HGNC:30634): (SREBF chaperone) This gene encodes a protein with a sterol sensing domain (SSD) and seven WD domains. In the presence of cholesterol, this protein binds to sterol regulatory element binding proteins (SREBPs) and mediates their transport from the ER to the Golgi. The SREBPs are then proteolytically cleaved and regulate sterol biosynthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.38319468).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1422896Hom.: 0 Cov.: 66 AF XY: 0.00 AC XY: 0AN XY: 704392
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1422896
Hom.:
Cov.:
66
AF XY:
AC XY:
0
AN XY:
704392
African (AFR)
AF:
AC:
0
AN:
32564
American (AMR)
AF:
AC:
0
AN:
39354
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25374
East Asian (EAS)
AF:
AC:
0
AN:
37574
South Asian (SAS)
AF:
AC:
0
AN:
81428
European-Finnish (FIN)
AF:
AC:
0
AN:
48996
Middle Eastern (MID)
AF:
AC:
0
AN:
5716
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1092966
Other (OTH)
AF:
AC:
0
AN:
58924
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
PhyloP100
Sift4G
Pathogenic
D
Vest4
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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