13-37590308-G-C

Variant names:

• chr13-37590308-G-C
• rs1006416
• NM_006475.3:c.441+64C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006475.3(POSTN):​c.441+64C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: POSTN NM_006475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 5 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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.441+64C>G		intron	N/A	NP_006466.2
	POSTN	NM_001286665.2		c.441+64C>G		intron	N/A	NP_001273594.1
	POSTN	NM_001330517.2		c.441+64C>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.441+64C>G		intron	N/A	ENSP00000369071.4
	POSTN	ENST00000379743.8	TSL:1	c.441+64C>G		intron	N/A	ENSP00000369067.4
	POSTN	ENST00000541179.5	TSL:1	c.441+64C>G		intron	N/A	ENSP00000437959.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1132582 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 561850

African (AFR) AF: 0.00 AC: 0 AN: 24960

American (AMR) AF: 0.00 AC: 0 AN: 23554

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20038

East Asian (EAS) AF: 0.00 AC: 0 AN: 33830

South Asian (SAS) AF: 0.00 AC: 0 AN: 57276

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44750

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4572

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 875234

Other (OTH) AF: 0.00 AC: 0 AN: 48368

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.37
DANN	Benign	0.59
PhyloP100		-0.77

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: rs1006416; hg19: chr13-38164445;