NM_002831.6:c.547A>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002831.6(PTPN6):c.547A>T(p.Thr183Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002831.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249584Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135410
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461886Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727244
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.547A>T (p.T183S) alteration is located in exon 5 (coding exon 5) of the PTPN6 gene. This alteration results from a A to T substitution at nucleotide position 547, causing the threonine (T) at amino acid position 183 to be replaced by a serine (S). 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