rs761011
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007050.6(PTPRT):c.860-9692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,164 control chromosomes in the GnomAD database, including 2,226 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 0.14 ( 2226 hom., cov: 32)
Exomes 𝑓: 0.33 ( 0 hom. )
Consequence
PTPRT
NM_007050.6 intron
NM_007050.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.143
Genes affected
PTPRT (HGNC:9682): (protein tyrosine phosphatase receptor type T) 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 possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, 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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRT | NM_007050.6 | c.860-9692C>T | intron_variant | ENST00000373187.6 | |||
LOC101927159 | NR_110004.1 | n.1284G>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRT | ENST00000373187.6 | c.860-9692C>T | intron_variant | 1 | NM_007050.6 | P4 | |||
ENST00000457704.2 | n.1284G>A | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.143 AC: 21698AN: 152040Hom.: 2212 Cov.: 32
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GnomAD4 exome AF: 0.333 AC: 2AN: 6Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2AN XY: 4
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GnomAD4 genome ? AF: 0.143 AC: 21744AN: 152158Hom.: 2226 Cov.: 32 AF XY: 0.138 AC XY: 10254AN XY: 74382
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ClinVar
Not reported inComputational 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