chr9-8389343-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002839.4(PTPRD):c.4275T>C(p.Tyr1425=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,613,128 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 55 hom., cov: 31)
Exomes 𝑓: 0.0015 ( 54 hom. )
Consequence
PTPRD
NM_002839.4 synonymous
NM_002839.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.959
Genes affected
PTPRD (HGNC:9668): (protein tyrosine phosphatase receptor type D) 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 three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 9-8389343-A-G is Benign according to our data. Variant chr9-8389343-A-G is described in ClinVar as [Benign]. Clinvar id is 784509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0141 (2144/152236) while in subpopulation AFR AF= 0.0493 (2048/41536). AF 95% confidence interval is 0.0475. There are 55 homozygotes in gnomad4. There are 1010 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2124 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRD | NM_002839.4 | c.4275T>C | p.Tyr1425= | synonymous_variant | 37/46 | ENST00000381196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRD | ENST00000381196.9 | c.4275T>C | p.Tyr1425= | synonymous_variant | 37/46 | 5 | NM_002839.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0140 AC: 2124AN: 152118Hom.: 52 Cov.: 31
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GnomAD3 exomes AF: 0.00376 AC: 943AN: 250492Hom.: 17 AF XY: 0.00292 AC XY: 396AN XY: 135418
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GnomAD4 exome AF: 0.00148 AC: 2156AN: 1460892Hom.: 54 Cov.: 30 AF XY: 0.00130 AC XY: 943AN XY: 726770
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GnomAD4 genome ? AF: 0.0141 AC: 2144AN: 152236Hom.: 55 Cov.: 31 AF XY: 0.0136 AC XY: 1010AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
PTPRD-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at