chr13-37593877-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000379747.9(POSTN):​c.219-1713C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,424 control chromosomes in the GnomAD database, including 26,933 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 0.59 ( 26933 hom., cov: 33)

Consequence

POSTN
ENST00000379747.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.327
Variant links:
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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
POSTNNM_006475.3 linkuse as main transcriptc.219-1713C>A intron_variant ENST00000379747.9 NP_006466.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
POSTNENST00000379747.9 linkuse as main transcriptc.219-1713C>A intron_variant 1 NM_006475.3 ENSP00000369071 P3Q15063-1

Frequencies

GnomAD3 genomes
AF:
0.591
AC:
89462
AN:
151294
Hom.:
26904
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.653
Gnomad AMI
AF:
0.405
Gnomad AMR
AF:
0.582
Gnomad ASJ
AF:
0.648
Gnomad EAS
AF:
0.847
Gnomad SAS
AF:
0.637
Gnomad FIN
AF:
0.498
Gnomad MID
AF:
0.505
Gnomad NFE
AF:
0.548
Gnomad OTH
AF:
0.579
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.591
AC:
89547
AN:
151424
Hom.:
26933
Cov.:
33
AF XY:
0.589
AC XY:
43559
AN XY:
73962
show subpopulations
Gnomad4 AFR
AF:
0.653
Gnomad4 AMR
AF:
0.582
Gnomad4 ASJ
AF:
0.648
Gnomad4 EAS
AF:
0.847
Gnomad4 SAS
AF:
0.636
Gnomad4 FIN
AF:
0.498
Gnomad4 NFE
AF:
0.548
Gnomad4 OTH
AF:
0.579
Alfa
AF:
0.581
Hom.:
3251
Bravo
AF:
0.603
Asia WGS
AF:
0.712
AC:
2425
AN:
3410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.8
DANN
Benign
0.24

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7321492; hg19: chr13-38168014; COSMIC: COSV65714413; API