rs2241743
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003728.4(UNC5C):c.2452-41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,596,656 control chromosomes in the GnomAD database, including 253,923 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 0.56 ( 24194 hom., cov: 33)
Exomes 𝑓: 0.56 ( 229729 hom. )
Consequence
UNC5C
NM_003728.4 intron
NM_003728.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0330
Genes affected
UNC5C (HGNC:12569): (unc-5 netrin receptor C) This gene product belongs to the UNC-5 family of netrin receptors. Netrins are secreted proteins that direct axon extension and cell migration during neural development. They are bifunctional proteins that act as attractants for some cell types and as repellents for others, and these opposite actions are thought to be mediated by two classes of receptors. The UNC-5 family of receptors mediate the repellent response to netrin; they are transmembrane proteins containing 2 immunoglobulin (Ig)-like domains and 2 type I thrombospondin motifs in the extracellular region. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC5C | NM_003728.4 | c.2452-41C>T | intron_variant | ENST00000453304.6 | |||
UNC5C | XM_005263321.4 | c.2509-41C>T | intron_variant | ||||
UNC5C | XM_047416345.1 | c.1408-41C>T | intron_variant | ||||
UNC5C | XM_047416346.1 | c.1408-41C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC5C | ENST00000453304.6 | c.2452-41C>T | intron_variant | 1 | NM_003728.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.561 AC: 85190AN: 151924Hom.: 24168 Cov.: 33
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GnomAD3 exomes AF: 0.554 AC: 135578AN: 244652Hom.: 39002 AF XY: 0.543 AC XY: 71725AN XY: 132140
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GnomAD4 exome AF: 0.560 AC: 808573AN: 1444614Hom.: 229729 Cov.: 31 AF XY: 0.554 AC XY: 396492AN XY: 715630
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GnomAD4 genome AF: 0.561 AC: 85267AN: 152042Hom.: 24194 Cov.: 33 AF XY: 0.559 AC XY: 41555AN XY: 74298
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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