chr20-50581309-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_002827.4(PTPN1):c.1133G>A(p.Ser378Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002827.4 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 |
---|---|---|---|---|---|---|---|
PTPN1 | NM_002827.4 | c.1133G>A | p.Ser378Asn | missense_variant | 9/10 | ENST00000371621.5 | |
PTPN1 | NM_001278618.2 | c.914G>A | p.Ser305Asn | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN1 | ENST00000371621.5 | c.1133G>A | p.Ser378Asn | missense_variant | 9/10 | 1 | NM_002827.4 | P1 | |
PTPN1 | ENST00000541713.5 | c.914G>A | p.Ser305Asn | missense_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461382Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726890
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2022 | The c.1133G>A (p.S378N) alteration is located in exon 9 (coding exon 9) of the PTPN1 gene. This alteration results from a G to A substitution at nucleotide position 1133, causing the serine (S) at amino acid position 378 to be replaced by an asparagine (N). 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
Publications
No publications associated with this variant yet.