chr11-18729473-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_006906.2(PTPN5):c.1584G>A(p.Thr528Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000425 in 1,412,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
PTPN5
NM_006906.2 synonymous
NM_006906.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.16
Publications
2 publications found
Genes affected
PTPN5 (HGNC:9657): (protein tyrosine phosphatase non-receptor type 5) Enables phosphotyrosine residue binding activity. Predicted to be involved in peptidyl-tyrosine dephosphorylation. Predicted to act upstream of or within protein dephosphorylation. Predicted to be located in nucleoplasm. Predicted to be integral component of membrane. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP7
Synonymous conserved (PhyloP=-1.15 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000122 AC: 3AN: 246586 AF XY: 0.00000747 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
246586
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000425 AC: 6AN: 1412186Hom.: 0 Cov.: 26 AF XY: 0.00000283 AC XY: 2AN XY: 705612 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
6
AN:
1412186
Hom.:
Cov.:
26
AF XY:
AC XY:
2
AN XY:
705612
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
32684
American (AMR)
AF:
AC:
4
AN:
44650
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25856
East Asian (EAS)
AF:
AC:
0
AN:
39522
South Asian (SAS)
AF:
AC:
1
AN:
85434
European-Finnish (FIN)
AF:
AC:
0
AN:
48622
Middle Eastern (MID)
AF:
AC:
0
AN:
4950
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1071564
Other (OTH)
AF:
AC:
0
AN:
58904
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000088), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
-
Psychiatry Genetics Yale University
Significance:not provided
Review Status:no classification provided
Collection Method:literature only
- -
Computational 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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