NM_173050.5:c.1084+313A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173050.5(SCUBE1):c.1084+313A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,118 control chromosomes in the GnomAD database, including 2,940 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 0.19 ( 2940 hom., cov: 33)
Consequence
SCUBE1
NM_173050.5 intron
NM_173050.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.936
Publications
6 publications found
Genes affected
SCUBE1 (HGNC:13441): (signal peptide, CUB domain and EGF like domain containing 1) This gene encodes a cell surface glycoprotein that is a member of the SCUBE (signal peptide, CUB domain, EGF (epidermal growth factor)-like protein) family. Family members have an amino-terminal signal peptide, nine copies of EGF-like repeats and a CUB domain at the carboxyl terminus. This protein is expressed in platelets and endothelial cells and may play an important role in vascular biology. [provided by RefSeq, Oct 2011]
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.190 AC: 28845AN: 152000Hom.: 2935 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
28845
AN:
152000
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.190 AC: 28874AN: 152118Hom.: 2940 Cov.: 33 AF XY: 0.186 AC XY: 13856AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
28874
AN:
152118
Hom.:
Cov.:
33
AF XY:
AC XY:
13856
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
10150
AN:
41484
American (AMR)
AF:
AC:
1964
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
522
AN:
3472
East Asian (EAS)
AF:
AC:
337
AN:
5162
South Asian (SAS)
AF:
AC:
892
AN:
4826
European-Finnish (FIN)
AF:
AC:
1672
AN:
10578
Middle Eastern (MID)
AF:
AC:
36
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12905
AN:
67994
Other (OTH)
AF:
AC:
352
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1214
2428
3641
4855
6069
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
312
624
936
1248
1560
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
459
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.