14-88479162-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007039.4(PTPN21):c.2269A>T(p.Ile757Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,552,046 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_007039.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN21 | NM_007039.4 | c.2269A>T | p.Ile757Phe | missense_variant | 13/19 | ENST00000556564.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN21 | ENST00000556564.6 | c.2269A>T | p.Ile757Phe | missense_variant | 13/19 | 1 | NM_007039.4 | P1 | |
PTPN21 | ENST00000328736.7 | c.2269A>T | p.Ile757Phe | missense_variant | 12/18 | 1 | P1 | ||
PTPN21 | ENST00000554270.5 | n.2382A>T | non_coding_transcript_exon_variant | 12/17 | 1 | ||||
PTPN21 | ENST00000536337.5 | c.*2206A>T | 3_prime_UTR_variant, NMD_transcript_variant | 13/19 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000257 AC: 5AN: 194238Hom.: 0 AF XY: 0.0000381 AC XY: 4AN XY: 104888
GnomAD4 exome AF: 0.0000200 AC: 28AN: 1399946Hom.: 0 Cov.: 31 AF XY: 0.0000188 AC XY: 13AN XY: 691294
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.2269A>T (p.I757F) alteration is located in exon 13 (coding exon 12) of the PTPN21 gene. This alteration results from a A to T substitution at nucleotide position 2269, causing the isoleucine (I) at amino acid position 757 to be replaced by a phenylalanine (F). 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