Variant 13-37598759-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_006475.3(POSTN):c.-33C>G variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0953 in 1,608,544 control chromosomes in the GnomAD database, including 9,485 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 ( 804 hom., cov: 32)

Exomes 𝑓: 0.096 ( 8681 hom. )

Consequence

POSTN
NM_006475.3 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.72

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]

POSTN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.21).

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/exons	MANE	Protein	UniProt
POSTN	NM_006475.3 linkuse as main transcript	c.-33C>G		5_prime_UTR_premature_start_codon_gain_variant	1/23	ENST00000379747.9	NP_006466.2	Q15063-1A0A024RDS2
POSTN	NM_006475.3 linkuse as main transcript	c.-33C>G		5_prime_UTR_variant	1/23	ENST00000379747.9	NP_006466.2	Q15063-1A0A024RDS2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POSTN	ENST00000379747.9 linkuse as main transcript	c.-33C>G		5_prime_UTR_premature_start_codon_gain_variant	1/23	1	NM_006475.3	ENSP00000369071.4		Q15063-1
POSTN	ENST00000379747.9 linkuse as main transcript	c.-33C>G		5_prime_UTR_variant	1/23	1	NM_006475.3	ENSP00000369071.4		Q15063-1

Frequencies

GnomAD3 genomes

AF:

0.0851

AC:

12940

AN:

152012

Hom.:

803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0365

Gnomad AMI

AF:

0.0758

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.0329

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.0826

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0873

Gnomad OTH

AF:

0.0766

GnomAD3 exomes

AF:

0.114

AC:

28532

AN:

250116

Hom.:

2434

AF XY:

0.113

AC XY:

15339

AN XY:

135230

show subpopulations

Gnomad AFR exome

AF:

0.0361

Gnomad AMR exome

AF:

0.144

Gnomad ASJ exome

AF:

0.0343

Gnomad EAS exome

AF:

0.350

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.0830

Gnomad NFE exome

AF:

0.0847

Gnomad OTH exome

AF:

0.0937

GnomAD4 exome

AF:

0.0964

AC:

140365

AN:

1456414

Hom.:

8681

Cov.:

AF XY:

0.0974

AC XY:

70561

AN XY:

724524

show subpopulations

Gnomad4 AFR exome

AF:

0.0331

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.0340

Gnomad4 EAS exome

AF:

0.330

Gnomad4 SAS exome

AF:

0.141

Gnomad4 FIN exome

AF:

0.0874

Gnomad4 NFE exome

AF:

0.0868

Gnomad4 OTH exome

AF:

0.0992

GnomAD4 genome

AF:

0.0851

AC:

12940

AN:

152130

Hom.:

804

Cov.:

AF XY:

0.0884

AC XY:

6574

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0364

Gnomad4 AMR

AF:

0.120

Gnomad4 ASJ

AF:

0.0329

Gnomad4 EAS

AF:

0.339

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.0826

Gnomad4 NFE

AF:

0.0873

Gnomad4 OTH

AF:

0.0768

Alfa

AF:

0.0788

Hom.:

113

Bravo

AF:

0.0863

Asia WGS

AF:

0.221

AC:

767

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.21

CADD

Benign

DANN

Benign

0.94

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over