chr12-70534620-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001109754.4(PTPRB):c.6236G>A(p.Arg2079His) variant causes a missense change. The variant allele was found at a frequency of 0.00000616 in 1,460,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2079C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001109754.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246428Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133634
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460358Hom.: 0 Cov.: 32 AF XY: 0.00000964 AC XY: 7AN XY: 726296
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.6236G>A (p.R2079H) alteration is located in exon 31 (coding exon 31) of the PTPRB gene. This alteration results from a G to A substitution at nucleotide position 6236, causing the arginine (R) at amino acid position 2079 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at