rs142096878
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The ENST00000442510.8(PTPRC):c.3510-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 1,607,198 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000442510.8 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRC | NM_002838.5 | c.3510-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000442510.8 | NP_002829.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRC | ENST00000442510.8 | c.3510-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002838.5 | ENSP00000411355 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00153 AC: 232AN: 152066Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000332 AC: 83AN: 249822Hom.: 0 AF XY: 0.000311 AC XY: 42AN XY: 135126
GnomAD4 exome AF: 0.000160 AC: 233AN: 1455014Hom.: 1 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 724252
GnomAD4 genome AF: 0.00152 AC: 232AN: 152184Hom.: 1 Cov.: 32 AF XY: 0.00163 AC XY: 121AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 29, 2020 | - - |
PTPRC-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 02, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Immunodeficiency 104 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at