chr7-137286354-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002825.7(PTN):c.-1-31380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,952 control chromosomes in the GnomAD database, including 27,396 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 ( 27396 hom., cov: 32)
Consequence
PTN
NM_002825.7 intron
NM_002825.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.160
Publications
7 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTN | NM_002825.7 | c.-1-31380G>A | intron_variant | Intron 1 of 4 | ENST00000348225.7 | NP_002816.1 | ||
PTN | NM_001321387.3 | c.-1-31380G>A | 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.-1-31380G>A | intron_variant | Intron 1 of 4 | 1 | NM_002825.7 | ENSP00000341170.2 | |||
PTN | ENST00000699293.1 | c.-1-31380G>A | intron_variant | Intron 1 of 4 | ENSP00000514273.1 | |||||
PTN | ENST00000393083.2 | c.-1-31380G>A | intron_variant | Intron 1 of 5 | 5 | ENSP00000376798.2 |
Frequencies
GnomAD3 genomes AF: 0.593 AC: 89999AN: 151832Hom.: 27382 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
89999
AN:
151832
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.593 AC: 90039AN: 151952Hom.: 27396 Cov.: 32 AF XY: 0.589 AC XY: 43740AN XY: 74274 show subpopulations
GnomAD4 genome
AF:
AC:
90039
AN:
151952
Hom.:
Cov.:
32
AF XY:
AC XY:
43740
AN XY:
74274
show subpopulations
African (AFR)
AF:
AC:
20300
AN:
41430
American (AMR)
AF:
AC:
7476
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
2302
AN:
3470
East Asian (EAS)
AF:
AC:
2318
AN:
5156
South Asian (SAS)
AF:
AC:
3324
AN:
4824
European-Finnish (FIN)
AF:
AC:
6562
AN:
10550
Middle Eastern (MID)
AF:
AC:
177
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45748
AN:
67934
Other (OTH)
AF:
AC:
1264
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1873
3746
5619
7492
9365
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
758
1516
2274
3032
3790
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1810
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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