3-48409677-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001130082.3(PLXNB1):c.5833C>T(p.Arg1945Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,828 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1945H) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNB1 | NM_001130082.3 | c.5833C>T | p.Arg1945Cys | missense_variant | 33/38 | ENST00000296440.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNB1 | ENST00000296440.11 | c.5833C>T | p.Arg1945Cys | missense_variant | 33/38 | 1 | NM_001130082.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251254Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135846
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461668Hom.: 0 Cov.: 35 AF XY: 0.0000124 AC XY: 9AN XY: 727152
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2022 | The c.5833C>T (p.R1945C) alteration is located in exon 33 (coding exon 31) of the PLXNB1 gene. This alteration results from a C to T substitution at nucleotide position 5833, causing the arginine (R) at amino acid position 1945 to be replaced by a cysteine (C). 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