chr3-129585954-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015103.3(PLXND1):c.1849C>T(p.Pro617Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 1,613,970 control chromosomes in the GnomAD database, including 1,857 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_015103.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXND1 | NM_015103.3 | c.1849C>T | p.Pro617Ser | missense_variant, splice_region_variant | 5/36 | ENST00000324093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXND1 | ENST00000324093.9 | c.1849C>T | p.Pro617Ser | missense_variant, splice_region_variant | 5/36 | 1 | NM_015103.3 | P1 | |
PLXND1 | ENST00000505237.2 | c.505C>T | p.Pro169Ser | missense_variant | 4/4 | 5 | |||
PLXND1 | ENST00000505665.5 | c.328C>T | p.Pro110Ser | missense_variant, splice_region_variant, NMD_transcript_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0488 AC: 7427AN: 152202Hom.: 264 Cov.: 33
GnomAD3 exomes AF: 0.0512 AC: 12874AN: 251336Hom.: 502 AF XY: 0.0525 AC XY: 7132AN XY: 135864
GnomAD4 exome AF: 0.0379 AC: 55342AN: 1461650Hom.: 1594 Cov.: 33 AF XY: 0.0395 AC XY: 28755AN XY: 727136
GnomAD4 genome AF: 0.0488 AC: 7438AN: 152320Hom.: 263 Cov.: 33 AF XY: 0.0502 AC XY: 3741AN XY: 74486
ClinVar
Submissions by phenotype
PLXND1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at