chr3-157437762-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002852.4(PTX3):c.380C>T(p.Ala127Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000749 in 1,334,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A127E) has been classified as Uncertain significance.
Frequency
Consequence
NM_002852.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTX3 | ENST00000295927.4 | c.380C>T | p.Ala127Val | missense_variant | Exon 2 of 3 | 1 | NM_002852.4 | ENSP00000295927.3 | ||
VEPH1 | ENST00000362010.7 | c.530-9274G>A | intron_variant | Intron 4 of 13 | 1 | NM_001167912.2 | ENSP00000354919.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.49e-7 AC: 1AN: 1334864Hom.: 0 Cov.: 35 AF XY: 0.00000152 AC XY: 1AN XY: 657990
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at