3-126988624-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_032242.4(PLXNA1):c.31C>T(p.Leu11Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000153 in 1,569,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. L11L) has been classified as Likely benign.
Frequency
Consequence
NM_032242.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLXNA1 | ENST00000393409.3 | c.31C>T | p.Leu11Phe | missense_variant | Exon 2 of 32 | 1 | NM_032242.4 | ENSP00000377061.2 | ||
PLXNA1 | ENST00000684469.1 | c.31C>T | p.Leu11Phe | missense_variant | Exon 2 of 2 | ENSP00000507976.1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152256Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000150 AC: 3AN: 200534Hom.: 0 AF XY: 0.00000920 AC XY: 1AN XY: 108688
GnomAD4 exome AF: 0.00000847 AC: 12AN: 1416804Hom.: 0 Cov.: 32 AF XY: 0.00000571 AC XY: 4AN XY: 700330
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152256Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74380
ClinVar
Submissions by phenotype
PLXNA1-related disorder Uncertain:1
The PLXNA1 c.31C>T variant is predicted to result in the amino acid substitution p.Leu11Phe. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.028% of alleles in individuals of African descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at