14-88479102-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007039.4(PTPN21):c.2329G>A(p.Val777Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,574,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN21 | NM_007039.4 | c.2329G>A | p.Val777Ile | missense_variant | 13/19 | ENST00000556564.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN21 | ENST00000556564.6 | c.2329G>A | p.Val777Ile | missense_variant | 13/19 | 1 | NM_007039.4 | P1 | |
PTPN21 | ENST00000328736.7 | c.2329G>A | p.Val777Ile | missense_variant | 12/18 | 1 | P1 | ||
PTPN21 | ENST00000554270.5 | n.2442G>A | non_coding_transcript_exon_variant | 12/17 | 1 | ||||
PTPN21 | ENST00000536337.5 | c.*2266G>A | 3_prime_UTR_variant, NMD_transcript_variant | 13/19 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000184 AC: 4AN: 217040Hom.: 0 AF XY: 0.0000254 AC XY: 3AN XY: 117908
GnomAD4 exome AF: 0.0000562 AC: 80AN: 1422602Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 31AN XY: 704634
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.2329G>A (p.V777I) alteration is located in exon 13 (coding exon 12) of the PTPN21 gene. This alteration results from a G to A substitution at nucleotide position 2329, causing the valine (V) at amino acid position 777 to be replaced by an isoleucine (I). 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