GeneBe

rs12677663

Variant names:

Variant summary

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

The ENST00000519697.1(SBSPON):​n.583-13899C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,514 control chromosomes in the GnomAD database, including 32,607 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 0.65 ( 32607 hom., cov: 28)

Consequence

SBSPON
ENST00000519697.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347

Publications

24 publications found
Variant links:
Genes affected
SBSPON (HGNC:30362): (somatomedin B and thrombospondin type 1 domain containing) Predicted to be an extracellular matrix structural constituent. Colocalizes with collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SBSPONENST00000519697.1 linkn.583-13899C>A intron_variant Intron 1 of 4 2

Frequencies

GnomAD3 genomes
AF:
0.650
AC:
98416
AN:
151396
Hom.:
32551
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.778
Gnomad AMI
AF:
0.609
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.654
Gnomad EAS
AF:
0.836
Gnomad SAS
AF:
0.675
Gnomad FIN
AF:
0.572
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.580
Gnomad OTH
AF:
0.669
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.650
AC:
98532
AN:
151514
Hom.:
32607
Cov.:
28
AF XY:
0.653
AC XY:
48299
AN XY:
73970
show subpopulations
African (AFR)
AF:
0.779
AC:
32178
AN:
41332
American (AMR)
AF:
0.597
AC:
9073
AN:
15192
Ashkenazi Jewish (ASJ)
AF:
0.654
AC:
2267
AN:
3464
East Asian (EAS)
AF:
0.837
AC:
4304
AN:
5144
South Asian (SAS)
AF:
0.676
AC:
3213
AN:
4754
European-Finnish (FIN)
AF:
0.572
AC:
5992
AN:
10468
Middle Eastern (MID)
AF:
0.670
AC:
197
AN:
294
European-Non Finnish (NFE)
AF:
0.580
AC:
39342
AN:
67858
Other (OTH)
AF:
0.673
AC:
1412
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1658
3315
4973
6630
8288
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
792
1584
2376
3168
3960
<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:
0.607
Hom.:
111730
Bravo
AF:
0.657
Asia WGS
AF:
0.756
AC:
2630
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.58
DANN
Benign
0.46
PhyloP100
-0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12677663; hg19: chr8-74007347; API