chrX-154467904-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_017514.5(PLXNA3):c.3723C>A(p.Ala1241=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A1241A) has been classified as Benign.
Frequency
Consequence
NM_017514.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNA3 | NM_017514.5 | c.3723C>A | p.Ala1241= | synonymous_variant | 21/33 | ENST00000369682.4 | |
PLXNA3 | XM_047442247.1 | c.3565C>A | p.Leu1189Ile | missense_variant | 21/22 | ||
PLXNA3 | XR_007068193.1 | n.3898C>A | non_coding_transcript_exon_variant | 21/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNA3 | ENST00000369682.4 | c.3723C>A | p.Ala1241= | synonymous_variant | 21/33 | 1 | NM_017514.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000456 AC: 5AN: 1096763Hom.: 0 Cov.: 53 AF XY: 0.00000551 AC XY: 2AN XY: 362761
GnomAD4 genome ? Cov.: 23
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at