13-37585496-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006475.3(POSTN):c.896-568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 152,276 control chromosomes in the GnomAD database, including 808 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 0.085 ( 808 hom., cov: 32)
Consequence
POSTN
NM_006475.3 intron
NM_006475.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.140
Publications
4 publications found
Genes affected
POSTN (HGNC:16953): (periostin) This gene encodes a secreted extracellular matrix protein that functions in tissue development and regeneration, including wound healing, and ventricular remodeling following myocardial infarction. The encoded protein binds to integrins to support adhesion and migration of epithelial cells. This protein plays a role in cancer stem cell maintenance and metastasis. Mice lacking this gene exhibit cardiac valve disease, and skeletal and dental defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2015]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POSTN | NM_006475.3 | c.896-568T>C | intron_variant | Intron 7 of 22 | ENST00000379747.9 | NP_006466.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0855 AC: 13009AN: 152158Hom.: 806 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
13009
AN:
152158
Hom.:
Cov.:
32
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: 0.0855 AC: 13015AN: 152276Hom.: 808 Cov.: 32 AF XY: 0.0890 AC XY: 6629AN XY: 74452 show subpopulations
GnomAD4 genome
AF:
AC:
13015
AN:
152276
Hom.:
Cov.:
32
AF XY:
AC XY:
6629
AN XY:
74452
show subpopulations
African (AFR)
AF:
AC:
1547
AN:
41556
American (AMR)
AF:
AC:
1849
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
115
AN:
3470
East Asian (EAS)
AF:
AC:
1755
AN:
5174
South Asian (SAS)
AF:
AC:
684
AN:
4828
European-Finnish (FIN)
AF:
AC:
880
AN:
10620
Middle Eastern (MID)
AF:
AC:
11
AN:
294
European-Non Finnish (NFE)
AF:
AC:
5940
AN:
68022
Other (OTH)
AF:
AC:
165
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
606
1213
1819
2426
3032
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
152
304
456
608
760
<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:
781
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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