chr3-48409714-G-A
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001130082.3(PLXNB1):c.5796C>T(p.Phe1932=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,613,646 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.011 ( 29 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 34 hom. )
Consequence
PLXNB1
NM_001130082.3 synonymous
NM_001130082.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.147
Genes affected
PLXNB1 (HGNC:9103): (plexin B1) Enables semaphorin receptor activity. Involved in several processes, including negative regulation of cell adhesion; regulation of cell shape; and semaphorin-plexin signaling pathway. Is integral component of plasma membrane. Part of semaphorin receptor complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 3-48409714-G-A is Benign according to our data. Variant chr3-48409714-G-A is described in ClinVar as [Benign]. Clinvar id is 785050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.147 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0113 (1713/152252) while in subpopulation AFR AF= 0.0396 (1645/41544). AF 95% confidence interval is 0.038. There are 29 homozygotes in gnomad4. There are 792 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1713 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXNB1 | NM_001130082.3 | c.5796C>T | p.Phe1932= | synonymous_variant | 33/38 | ENST00000296440.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXNB1 | ENST00000296440.11 | c.5796C>T | p.Phe1932= | synonymous_variant | 33/38 | 1 | NM_001130082.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0112 AC: 1710AN: 152134Hom.: 29 Cov.: 32
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GnomAD3 exomes AF: 0.00305 AC: 766AN: 250802Hom.: 21 AF XY: 0.00214 AC XY: 290AN XY: 135614
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GnomAD4 exome AF: 0.00124 AC: 1806AN: 1461394Hom.: 34 Cov.: 35 AF XY: 0.00104 AC XY: 759AN XY: 726994
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GnomAD4 genome AF: 0.0113 AC: 1713AN: 152252Hom.: 29 Cov.: 32 AF XY: 0.0106 AC XY: 792AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
PLXNB1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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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