NM_173050.5:c.485-340A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173050.5(SCUBE1):​c.485-340A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,108 control chromosomes in the GnomAD database, including 2,572 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 0.16 ( 2572 hom., cov: 32)

Consequence

SCUBE1
NM_173050.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58

Publications

1 publications found
Variant links:
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCUBE1NM_173050.5 linkc.485-340A>T intron_variant Intron 4 of 21 ENST00000360835.9 NP_766638.2 Q8IWY4Q86TI6Q6ZS56A0JP65
LOC124905129XR_007068120.1 linkn.3850T>A non_coding_transcript_exon_variant Exon 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCUBE1ENST00000360835.9 linkc.485-340A>T intron_variant Intron 4 of 21 1 NM_173050.5 ENSP00000354080.3 Q8IWY4
SCUBE1ENST00000290460.7 linkc.485-340A>T intron_variant Intron 4 of 7 1 ENSP00000290460.7 B1AH90

Frequencies

GnomAD3 genomes
AF:
0.165
AC:
25043
AN:
151988
Hom.:
2566
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0811
Gnomad AMI
AF:
0.182
Gnomad AMR
AF:
0.289
Gnomad ASJ
AF:
0.161
Gnomad EAS
AF:
0.361
Gnomad SAS
AF:
0.219
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.165
Gnomad OTH
AF:
0.197
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.165
AC:
25044
AN:
152108
Hom.:
2572
Cov.:
32
AF XY:
0.170
AC XY:
12643
AN XY:
74340
show subpopulations
African (AFR)
AF:
0.0808
AC:
3354
AN:
41522
American (AMR)
AF:
0.289
AC:
4415
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.161
AC:
560
AN:
3470
East Asian (EAS)
AF:
0.361
AC:
1859
AN:
5150
South Asian (SAS)
AF:
0.217
AC:
1042
AN:
4808
European-Finnish (FIN)
AF:
0.183
AC:
1938
AN:
10586
Middle Eastern (MID)
AF:
0.224
AC:
66
AN:
294
European-Non Finnish (NFE)
AF:
0.165
AC:
11214
AN:
67962
Other (OTH)
AF:
0.204
AC:
430
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1030
2059
3089
4118
5148
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
272
544
816
1088
1360
<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:
0.149
Hom.:
233
Bravo
AF:
0.172
Asia WGS
AF:
0.326
AC:
1132
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.16
DANN
Benign
0.58
PhyloP100
-1.6
PromoterAI
0.0040
Neutral
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs5759236; hg19: chr22-43659191; API