chr12-70555206-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001109754.4(PTPRB):c.5097C>G(p.Thr1699=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00376 in 1,613,860 control chromosomes in the GnomAD database, including 210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 102 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 108 hom. )
Consequence
PTPRB
NM_001109754.4 synonymous
NM_001109754.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.13
Genes affected
PTPRB (HGNC:9665): (protein tyrosine phosphatase receptor type B) 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 domain, a single transmembrane segment and one intracytoplasmic catalytic domain, thus belongs to receptor type PTP. The extracellular region of this PTP is composed of multiple fibronectin type_III repeats, which was shown to interact with neuronal receptor and cell adhesion molecules, such as contactin and tenascin C. This protein was also found to interact with sodium channels, and thus may regulate sodium channels by altering tyrosine phosphorylation status. The functions of the interaction partners of this protein implicate the roles of this PTP in cell adhesion, neurite growth, and neuronal differentiation. Alternate transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 12-70555206-G-C is Benign according to our data. Variant chr12-70555206-G-C is described in ClinVar as [Benign]. Clinvar id is 710173.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.13 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRB | NM_001109754.4 | c.5097C>G | p.Thr1699= | synonymous_variant | 20/34 | ENST00000334414.11 | |
LOC105369828 | XR_001749196.2 | n.10007-2774G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRB | ENST00000334414.11 | c.5097C>G | p.Thr1699= | synonymous_variant | 20/34 | 1 | NM_001109754.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0195 AC: 2971AN: 152110Hom.: 102 Cov.: 33
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GnomAD3 exomes AF: 0.00480 AC: 1194AN: 248934Hom.: 36 AF XY: 0.00364 AC XY: 492AN XY: 135016
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GnomAD4 exome AF: 0.00211 AC: 3087AN: 1461632Hom.: 108 Cov.: 31 AF XY: 0.00182 AC XY: 1320AN XY: 727102
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GnomAD4 genome ? AF: 0.0196 AC: 2979AN: 152228Hom.: 102 Cov.: 33 AF XY: 0.0189 AC XY: 1410AN XY: 74418
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 02, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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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