13-37579214-T-C

Variant names:

• chr13-37579214-T-C
• rs7323378
• NM_006475.3:c.1791+15A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006475.3(POSTN):​c.1791+15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,607,450 control chromosomes in the GnomAD database, including 159,223 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 0.43 (14151 hom., cov: 33)
  • Exomes 𝑓: 0.44 (145072 hom.)
• Consequence: POSTN NM_006475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 11 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006475.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POSTN	NM_006475.3	MANE Select	c.1791+15A>G		intron	N/A	NP_006466.2
	POSTN	NM_001286665.2		c.1791+15A>G		intron	N/A	NP_001273594.1
	POSTN	NM_001330517.2		c.1791+15A>G		intron	N/A	NP_001317446.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POSTN	ENST00000379747.9	TSL:1 MANE Select	c.1791+15A>G		intron	N/A	ENSP00000369071.4
	POSTN	ENST00000379743.8	TSL:1	c.1791+15A>G		intron	N/A	ENSP00000369067.4
	POSTN	ENST00000541179.5	TSL:1	c.1791+15A>G		intron	N/A	ENSP00000437959.1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64686 AN: 151938 Hom.: 14140 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.435

GnomAD2 exomes AF: 0.414 AC: 103622 AN: 250162 AF XY: 0.416

Gnomad AFR exome AF: 0.394

Gnomad AMR exome AF: 0.426

Gnomad ASJ exome AF: 0.351

Gnomad EAS exome AF: 0.136

Gnomad FIN exome AF: 0.506

Gnomad NFE exome AF: 0.454

Gnomad OTH exome AF: 0.427

GnomAD4 exome AF: 0.443 AC: 644772 AN: 1455394 Hom.: 145072 Cov.: 37 AF XY: 0.441 AC XY: 319804 AN XY: 724396

African (AFR) AF: 0.395 AC: 13156 AN: 33334

American (AMR) AF: 0.424 AC: 18938 AN: 44662

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 9206 AN: 26076

East Asian (EAS) AF: 0.203 AC: 8008 AN: 39518

South Asian (SAS) AF: 0.389 AC: 33501 AN: 86086

European-Finnish (FIN) AF: 0.496 AC: 26411 AN: 53204

Middle Eastern (MID) AF: 0.496 AC: 2856 AN: 5758

European-Non Finnish (NFE) AF: 0.459 AC: 507711 AN: 1106566

Other (OTH) AF: 0.415 AC: 24985 AN: 60190

GnomAD4 genome AF: 0.426 AC: 64726 AN: 152056 Hom.: 14151 Cov.: 33 AF XY: 0.428 AC XY: 31791 AN XY: 74332

African (AFR) AF: 0.395 AC: 16398 AN: 41462

American (AMR) AF: 0.424 AC: 6475 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3472

East Asian (EAS) AF: 0.152 AC: 787 AN: 5170

South Asian (SAS) AF: 0.369 AC: 1781 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5387 AN: 10570

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31058 AN: 67962

Other (OTH) AF: 0.435 AC: 916 AN: 2108

Alfa AF: 0.446 Hom.: 51325

Bravo AF: 0.416

Asia WGS AF: 0.290 AC: 1010 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7323378; hg19: chr13-38153351; COSMIC: COSV65713118;