chr1-202152612-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002832.4(PTPN7):c.805C>T(p.Arg269Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. R269H) has been classified as Uncertain significance.
Frequency
Consequence
NM_002832.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN7 | NM_002832.4 | c.805C>T | p.Arg269Cys | missense_variant | 8/10 | ENST00000691036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN7 | ENST00000691036.1 | c.805C>T | p.Arg269Cys | missense_variant | 8/10 | NM_002832.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251042Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135834
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461708Hom.: 0 Cov.: 32 AF XY: 0.000149 AC XY: 108AN XY: 727142
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.1120C>T (p.R374C) alteration is located in exon 8 (coding exon 8) of the PTPN7 gene. This alteration results from a C to T substitution at nucleotide position 1120, causing the arginine (R) at amino acid position 374 to be replaced by a cysteine (C). 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