19-5208308-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_002850.4(PTPRS):c.5571C>T(p.Ile1857Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,613,982 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.0012 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0017 ( 64 hom. )
Consequence
PTPRS
NM_002850.4 synonymous
NM_002850.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.451
Genes affected
PTPRS (HGNC:9681): (protein tyrosine phosphatase receptor type S) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of multiple Ig-like and fibronectin type III-like domains. Studies of the similar gene in mice suggested that this PTP may be involved in cell-cell interaction, primary axonogenesis, and axon guidance during embryogenesis. This PTP has been also implicated in the molecular control of adult nerve repair. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 19-5208308-G-A is Benign according to our data. Variant chr19-5208308-G-A is described in ClinVar as [Benign]. Clinvar id is 3041878.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.451 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00118 (179/152320) while in subpopulation SAS AF= 0.0263 (127/4832). AF 95% confidence interval is 0.0226. There are 3 homozygotes in gnomad4. There are 124 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 179 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 179AN: 152202Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00379 AC: 952AN: 251138Hom.: 26 AF XY: 0.00477 AC XY: 647AN XY: 135718
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GnomAD4 exome AF: 0.00171 AC: 2496AN: 1461662Hom.: 64 Cov.: 32 AF XY: 0.00233 AC XY: 1694AN XY: 727132
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GnomAD4 genome AF: 0.00118 AC: 179AN: 152320Hom.: 3 Cov.: 33 AF XY: 0.00166 AC XY: 124AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
PTPRS-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at