rs9547965
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006475.3(POSTN):c.1660+110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 1,225,784 control chromosomes in the GnomAD database, including 40,630 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 0.22 ( 3959 hom., cov: 33)
Exomes 𝑓: 0.26 ( 36671 hom. )
Consequence
POSTN
NM_006475.3 intron
NM_006475.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.155
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POSTN | NM_006475.3 | c.1660+110C>T | intron_variant | ENST00000379747.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POSTN | ENST00000379747.9 | c.1660+110C>T | intron_variant | 1 | NM_006475.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.215 AC: 32743AN: 151954Hom.: 3959 Cov.: 33
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GnomAD4 exome AF: 0.256 AC: 274513AN: 1073712Hom.: 36671 AF XY: 0.253 AC XY: 135441AN XY: 535398
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GnomAD4 genome ? AF: 0.215 AC: 32757AN: 152072Hom.: 3959 Cov.: 33 AF XY: 0.216 AC XY: 16018AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at