rs865569
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_005761.3(PLXNC1):c.3087+31T>C variant causes a intron change. The variant allele was found at a frequency of 0.821 in 1,397,062 control chromosomes in the GnomAD database, including 473,782 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.78 ( 46709 hom., cov: 34)
Exomes 𝑓: 0.83 ( 427073 hom. )
Consequence
PLXNC1
NM_005761.3 intron
NM_005761.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.58
Genes affected
PLXNC1 (HGNC:9106): (plexin C1) This gene encodes a member of the plexin family. Plexins are transmembrane receptors for semaphorins, a large family of proteins that regulate axon guidance, cell motility and migration, and the immune response. The encoded protein and its ligand regulate melanocyte adhesion, and viral semaphorins may modulate the immune response by binding to this receptor. The encoded protein may be a tumor suppressor protein for melanoma. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.22).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNC1 | NM_005761.3 | c.3087+31T>C | intron_variant | ENST00000258526.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNC1 | ENST00000258526.9 | c.3087+31T>C | intron_variant | 1 | NM_005761.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.778 AC: 118368AN: 152120Hom.: 46694 Cov.: 34
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GnomAD3 exomes AF: 0.796 AC: 198874AN: 249868Hom.: 79955 AF XY: 0.801 AC XY: 108257AN XY: 135102
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GnomAD4 exome AF: 0.826 AC: 1028519AN: 1244824Hom.: 427073 Cov.: 17 AF XY: 0.826 AC XY: 520714AN XY: 630640
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GnomAD4 genome ? AF: 0.778 AC: 118427AN: 152238Hom.: 46709 Cov.: 34 AF XY: 0.777 AC XY: 57842AN XY: 74450
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at