chr1-214364636-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005401.5(PTPN14):c.3311A>G(p.Asn1104Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. N1104N) has been classified as Benign.
Frequency
Consequence
NM_005401.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN14 | NM_005401.5 | c.3311A>G | p.Asn1104Ser | missense_variant | 18/19 | ENST00000366956.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN14 | ENST00000366956.10 | c.3311A>G | p.Asn1104Ser | missense_variant | 18/19 | 1 | NM_005401.5 | P1 | |
PTPN14 | ENST00000543945.5 | c.*2587A>G | 3_prime_UTR_variant | 17/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152036Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251128Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135734
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152036Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74238
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The c.3311A>G (p.N1104S) alteration is located in exon 18 (coding exon 17) of the PTPN14 gene. This alteration results from a A to G substitution at nucleotide position 3311, causing the asparagine (N) at amino acid position 1104 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