rs692843
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_133369.3(UNC5A):c.70+17825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,202 control chromosomes in the GnomAD database, including 49,725 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 0.75 ( 49725 hom., cov: 33)
Consequence
UNC5A
NM_133369.3 intron
NM_133369.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.779
Genes affected
UNC5A (HGNC:12567): (unc-5 netrin receptor A) UNC5A belongs to a family of netrin-1 (MIM 601614) receptors thought to mediate the chemorepulsive effect of netrin-1 on specific axons. For more information on UNC5 proteins, see UNC5C (MIM 603610).[supplied by OMIM, Apr 2004]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC5A | NM_133369.3 | c.70+17825G>A | intron_variant | ENST00000329542.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC5A | ENST00000329542.9 | c.70+17825G>A | intron_variant | 1 | NM_133369.3 | ||||
UNC5A | ENST00000509580.2 | c.70+17825G>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.753 AC: 114482AN: 152084Hom.: 49727 Cov.: 33
GnomAD3 genomes
?
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114482
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.752 AC: 114490AN: 152202Hom.: 49725 Cov.: 33 AF XY: 0.761 AC XY: 56621AN XY: 74430
GnomAD4 genome
?
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114490
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152202
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33
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AC XY:
56621
AN XY:
74430
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Asia WGS
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2959
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3478
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