rs3750050
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002835.4(PTPN12):āc.1717A>Gā(p.Thr573Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,613,716 control chromosomes in the GnomAD database, including 41,036 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002835.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN12 | NM_002835.4 | c.1717A>G | p.Thr573Ala | missense_variant | 13/18 | ENST00000248594.11 | NP_002826.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN12 | ENST00000248594.11 | c.1717A>G | p.Thr573Ala | missense_variant | 13/18 | 1 | NM_002835.4 | ENSP00000248594.6 | ||
PTPN12 | ENST00000415482.6 | c.1360A>G | p.Thr454Ala | missense_variant | 13/18 | 5 | ENSP00000392429.2 | |||
PTPN12 | ENST00000435495.6 | c.1327A>G | p.Thr443Ala | missense_variant | 12/17 | 2 | ENSP00000397991.2 | |||
PTPN12 | ENST00000407343.3 | c.241A>G | p.Thr81Ala | missense_variant | 1/4 | 3 | ENSP00000385079.3 |
Frequencies
GnomAD3 genomes AF: 0.220 AC: 33396AN: 152040Hom.: 4722 Cov.: 32
GnomAD3 exomes AF: 0.270 AC: 67842AN: 251242Hom.: 12860 AF XY: 0.265 AC XY: 36009AN XY: 135798
GnomAD4 exome AF: 0.190 AC: 278324AN: 1461558Hom.: 36312 Cov.: 34 AF XY: 0.194 AC XY: 141402AN XY: 727098
GnomAD4 genome AF: 0.220 AC: 33406AN: 152158Hom.: 4724 Cov.: 32 AF XY: 0.229 AC XY: 17015AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | This variant is associated with the following publications: (PMID: 30731403) - |
PTPN12-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at