chrX-154460370-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_017514.5(PLXNA3):āc.187C>Gā(p.Leu63Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 1,208,747 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_017514.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNA3 | NM_017514.5 | c.187C>G | p.Leu63Val | missense_variant | 2/33 | ENST00000369682.4 | |
PLXNA3 | XM_047442247.1 | c.187C>G | p.Leu63Val | missense_variant | 2/22 | ||
PLXNA3 | XR_007068193.1 | n.362C>G | non_coding_transcript_exon_variant | 2/32 | |||
PLXNA3 | XR_430556.4 | n.362C>G | non_coding_transcript_exon_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNA3 | ENST00000369682.4 | c.187C>G | p.Leu63Val | missense_variant | 2/33 | 1 | NM_017514.5 | P1 | |
PLXNA3 | ENST00000495040.1 | n.146-729C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000222 AC: 25AN: 112810Hom.: 0 Cov.: 25 AF XY: 0.000257 AC XY: 9AN XY: 34966
GnomAD3 exomes AF: 0.0000732 AC: 13AN: 177565Hom.: 0 AF XY: 0.0000312 AC XY: 2AN XY: 64033
GnomAD4 exome AF: 0.0000347 AC: 38AN: 1095937Hom.: 0 Cov.: 31 AF XY: 0.0000304 AC XY: 11AN XY: 361833
GnomAD4 genome AF: 0.000222 AC: 25AN: 112810Hom.: 0 Cov.: 25 AF XY: 0.000257 AC XY: 9AN XY: 34966
ClinVar
Submissions by phenotype
PLXNA3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 03, 2021 | This variant is classified as likely 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