chr4-95169360-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003728.4(UNC5C):c.2670C>T(p.Gly890Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000955 in 1,614,186 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00067 ( 3 hom. )
Consequence
UNC5C
NM_003728.4 synonymous
NM_003728.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.75
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 4-95169360-G-A is Benign according to our data. Variant chr4-95169360-G-A is described in ClinVar as [Benign]. Clinvar id is 786040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.75 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UNC5C | NM_003728.4 | c.2670C>T | p.Gly890Gly | synonymous_variant | 16/16 | ENST00000453304.6 | NP_003719.3 | |
UNC5C | XM_005263321.4 | c.2727C>T | p.Gly909Gly | synonymous_variant | 17/17 | XP_005263378.1 | ||
UNC5C | XM_047416345.1 | c.1626C>T | p.Gly542Gly | synonymous_variant | 18/18 | XP_047272301.1 | ||
UNC5C | XM_047416346.1 | c.1626C>T | p.Gly542Gly | synonymous_variant | 19/19 | XP_047272302.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UNC5C | ENST00000453304.6 | c.2670C>T | p.Gly890Gly | synonymous_variant | 16/16 | 1 | NM_003728.4 | ENSP00000406022.1 |
Frequencies
GnomAD3 genomes AF: 0.00372 AC: 566AN: 152200Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00133 AC: 332AN: 249432Hom.: 0 AF XY: 0.00105 AC XY: 142AN XY: 134990
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GnomAD4 exome AF: 0.000666 AC: 974AN: 1461868Hom.: 3 Cov.: 30 AF XY: 0.000622 AC XY: 452AN XY: 727224
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GnomAD4 genome AF: 0.00373 AC: 568AN: 152318Hom.: 1 Cov.: 33 AF XY: 0.00344 AC XY: 256AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 13, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at