chr14-88469010-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007039.4(PTPN21):c.3302A>G(p.Asn1101Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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.3302A>G | p.Asn1101Ser | missense_variant | 18/19 | ENST00000556564.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN21 | ENST00000556564.6 | c.3302A>G | p.Asn1101Ser | missense_variant | 18/19 | 1 | NM_007039.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251448Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135898
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727244
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2023 | The c.3302A>G (p.N1101S) alteration is located in exon 18 (coding exon 17) of the PTPN21 gene. This alteration results from a A to G substitution at nucleotide position 3302, causing the asparagine (N) at amino acid position 1101 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