rs2298872
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_002838.5(PTPRC):c.3853A>C(p.Ser1285Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000256 in 1,613,402 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002838.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250238Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135252
GnomAD4 exome AF: 0.000269 AC: 393AN: 1461164Hom.: 6 Cov.: 31 AF XY: 0.000248 AC XY: 180AN XY: 726896
GnomAD4 genome AF: 0.000131 AC: 20AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74426
ClinVar
Submissions by phenotype
Immunodeficiency 104 Uncertain:1
This sequence change replaces serine with arginine at codon 1285 of the PTPRC protein (p.Ser1285Arg). The serine residue is moderately conserved and there is a moderate physicochemical difference between serine and arginine. This variant is present in population databases (rs2298872, ExAC 0.2%). This variant has not been reported in the literature in individuals affected with PTPRC-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at