20-50581336-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002827.4(PTPN1):c.1160C>T(p.Pro387Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00583 in 1,614,032 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_002827.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00488 AC: 743AN: 152192Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00475 AC: 1194AN: 251178Hom.: 6 AF XY: 0.00493 AC XY: 670AN XY: 135782
GnomAD4 exome AF: 0.00593 AC: 8668AN: 1461722Hom.: 23 Cov.: 31 AF XY: 0.00580 AC XY: 4215AN XY: 727134
GnomAD4 genome AF: 0.00488 AC: 743AN: 152310Hom.: 3 Cov.: 32 AF XY: 0.00448 AC XY: 334AN XY: 74472
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at