3-48409421-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001130082.3(PLXNB1):āc.5995G>Cā(p.Val1999Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1999M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130082.3 missense
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 |
---|---|---|---|---|---|---|---|
PLXNB1 | NM_001130082.3 | c.5995G>C | p.Val1999Leu | missense_variant | 34/38 | ENST00000296440.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNB1 | ENST00000296440.11 | c.5995G>C | p.Val1999Leu | missense_variant | 34/38 | 1 | NM_001130082.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461870Hom.: 0 Cov.: 36 AF XY: 0.0000110 AC XY: 8AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.5995G>C (p.V1999L) alteration is located in exon 34 (coding exon 32) of the PLXNB1 gene. This alteration results from a G to C substitution at nucleotide position 5995, causing the valine (V) at amino acid position 1999 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at