16-1487448-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001328608.2(PTX4):c.664C>T(p.Pro222Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000469 in 1,514,334 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_001328608.2 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 |
---|---|---|---|---|---|---|---|
PTX4 | NM_001328608.2 | c.664C>T | p.Pro222Ser | missense_variant | 2/3 | ENST00000447419.7 | |
PTX4 | NM_001013658.1 | c.649C>T | p.Pro217Ser | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTX4 | ENST00000447419.7 | c.664C>T | p.Pro222Ser | missense_variant | 2/3 | 5 | NM_001328608.2 | A2 | |
PTX4 | ENST00000293922.1 | c.649C>T | p.Pro217Ser | missense_variant | 2/3 | 1 | P2 | ||
PTX4 | ENST00000440447.2 | c.351+313C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000179 AC: 3AN: 167908Hom.: 0 AF XY: 0.0000336 AC XY: 3AN XY: 89398
GnomAD4 exome AF: 0.0000477 AC: 65AN: 1362106Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 34AN XY: 667852
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.649C>T (p.P217S) alteration is located in exon 2 (coding exon 2) of the PTX4 gene. This alteration results from a C to T substitution at nucleotide position 649, causing the proline (P) at amino acid position 217 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