rs6468317
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_080872.4(UNC5D):c.103+151868T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00345 in 152,024 control chromosomes in the GnomAD database, including 7 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 0.0034 ( 7 hom., cov: 32)
Consequence
UNC5D
NM_080872.4 intron
NM_080872.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.474
Genes affected
UNC5D (HGNC:18634): (unc-5 netrin receptor D) Predicted to enable netrin receptor activity. Involved in cell-cell adhesion via plasma-membrane adhesion molecules. Predicted to be located in cell surface and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS2
?
High AC in GnomAd4 at 524 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC5D | NM_080872.4 | c.103+151868T>A | intron_variant | ENST00000404895.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC5D | ENST00000404895.7 | c.103+151868T>A | intron_variant | 1 | NM_080872.4 | P4 | |||
UNC5D | ENST00000287272.6 | c.103+151868T>A | intron_variant | 5 | |||||
UNC5D | ENST00000416672.5 | c.103+151868T>A | intron_variant | 5 | A1 | ||||
UNC5D | ENST00000420357.5 | c.103+151868T>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00346 AC: 525AN: 151906Hom.: 7 Cov.: 32
GnomAD3 genomes
?
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525
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151906
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00345 AC: 524AN: 152024Hom.: 7 Cov.: 32 AF XY: 0.00322 AC XY: 239AN XY: 74302
GnomAD4 genome
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524
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152024
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239
AN XY:
74302
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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