chr22-43253695-T-C
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.727+4524A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 140,678 control chromosomes in the GnomAD database, including 2,757 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 0.20 ( 2757 hom., cov: 31)
Consequence
SCUBE1
NM_173050.5 intron
NM_173050.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.457
Publications
5 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]
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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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCUBE1 | ENST00000360835.9 | c.727+4524A>G | intron_variant | Intron 6 of 21 | 1 | NM_173050.5 | ENSP00000354080.3 | |||
SCUBE1 | ENST00000290460.7 | c.817+1793A>G | intron_variant | Intron 7 of 7 | 1 | ENSP00000290460.7 | ||||
SCUBE1 | ENST00000449304.5 | c.286+1793A>G | intron_variant | Intron 3 of 4 | 5 | ENSP00000395327.1 |
Frequencies
GnomAD3 genomes AF: 0.201 AC: 28210AN: 140574Hom.: 2753 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
28210
AN:
140574
Hom.:
Cov.:
31
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: 0.201 AC: 28240AN: 140678Hom.: 2757 Cov.: 31 AF XY: 0.198 AC XY: 13667AN XY: 68876 show subpopulations
GnomAD4 genome
AF:
AC:
28240
AN:
140678
Hom.:
Cov.:
31
AF XY:
AC XY:
13667
AN XY:
68876
show subpopulations
African (AFR)
AF:
AC:
5937
AN:
33096
American (AMR)
AF:
AC:
2541
AN:
14780
Ashkenazi Jewish (ASJ)
AF:
AC:
541
AN:
3300
East Asian (EAS)
AF:
AC:
535
AN:
4890
South Asian (SAS)
AF:
AC:
1106
AN:
4736
European-Finnish (FIN)
AF:
AC:
1782
AN:
10304
Middle Eastern (MID)
AF:
AC:
42
AN:
282
European-Non Finnish (NFE)
AF:
AC:
15191
AN:
66432
Other (OTH)
AF:
AC:
393
AN:
2008
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1162
2324
3487
4649
5811
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
314
628
942
1256
1570
<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:
539
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
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