rs13245911

Variant names:

• chr7-137304859-G-A
• rs13245911
• NM_002825.7:c.-2+38580C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-137304859-G-A
• chr7-137304859-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002825.7(PTN):​c.-2+38580C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,762 control chromosomes in the GnomAD database, including 20,511 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 0.51 (20511 hom., cov: 31)
• Consequence: PTN NM_002825.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

Genes affected

PTN (HGNC:9630): (pleiotrophin) The protein encoded by this gene is a secreted heparin-binding growth factor. The protein has significant roles in cell growth and survival, cell migration, angiogenesis and tumorigenesis. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTN	NM_002825.7	c.-2+38580C>T		intron_variant	Intron 1 of 4	ENST00000348225.7	NP_002816.1
PTN	NM_001321387.3	c.-2+38580C>T		intron_variant	Intron 1 of 4		NP_001308316.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTN	ENST00000348225.7	c.-2+38580C>T		intron_variant	Intron 1 of 4	1	NM_002825.7	ENSP00000341170.2
PTN	ENST00000699293.1	c.-2+38580C>T		intron_variant	Intron 1 of 4			ENSP00000514273.1
PTN	ENST00000393083.2	c.-2+38580C>T		intron_variant	Intron 1 of 5	5		ENSP00000376798.2

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77570 AN: 151644 Hom.: 20501 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.523

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.511 AC: 77599 AN: 151762 Hom.: 20511 Cov.: 31 AF XY: 0.509 AC XY: 37748 AN XY: 74132

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.519

Alfa AF: 0.550 Hom.: 30326

Bravo AF: 0.489

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs13245911; hg19: chr7-136989606;