3-129556649-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015103.3(PLXND1):c.5629A>G(p.Ile1877Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000531 in 1,613,344 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_015103.3 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 |
---|---|---|---|---|---|---|---|
PLXND1 | NM_015103.3 | c.5629A>G | p.Ile1877Val | missense_variant | 35/36 | ENST00000324093.9 | |
PLXND1 | XM_011512588.3 | c.5629A>G | p.Ile1877Val | missense_variant | 35/36 | ||
PLXND1 | XM_011512589.2 | c.5239A>G | p.Ile1747Val | missense_variant | 32/33 | ||
PLXND1 | XM_011512592.1 | c.2797A>G | p.Ile933Val | missense_variant | 23/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXND1 | ENST00000324093.9 | c.5629A>G | p.Ile1877Val | missense_variant | 35/36 | 1 | NM_015103.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000460 AC: 70AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000268 AC: 67AN: 250092Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 135254
GnomAD4 exome AF: 0.000539 AC: 787AN: 1461180Hom.: 0 Cov.: 30 AF XY: 0.000513 AC XY: 373AN XY: 726862
GnomAD4 genome ? AF: 0.000460 AC: 70AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.000471 AC XY: 35AN XY: 74334
ClinVar
Submissions by phenotype
Kleine-Levin syndrome Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Undiagnosed Diseases Network, NIH | Oct 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at