rs9688032
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003062.4(SLIT3):c.413+64289A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,952 control chromosomes in the GnomAD database, including 10,019 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 0.36 ( 10019 hom., cov: 32)
Consequence
SLIT3
NM_003062.4 intron
NM_003062.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.183
Genes affected
SLIT3 (HGNC:11087): (slit guidance ligand 3) The protein encoded by this gene is secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLIT3 | NM_003062.4 | c.413+64289A>T | intron_variant | ENST00000519560.6 | |||
SLIT3 | NM_001271946.2 | c.413+64289A>T | intron_variant | ||||
SLIT3 | XM_017009779.1 | c.224+64289A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLIT3 | ENST00000519560.6 | c.413+64289A>T | intron_variant | 1 | NM_003062.4 | A1 | |||
SLIT3 | ENST00000332966.8 | c.413+64289A>T | intron_variant | 1 | P4 | ||||
SLIT3 | ENST00000518140.5 | n.450+64289A>T | intron_variant, non_coding_transcript_variant | 1 | |||||
SLIT3 | ENST00000521130.1 | n.482-8829A>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.359 AC: 54513AN: 151832Hom.: 10001 Cov.: 32
GnomAD3 genomes
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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: 0.359 AC: 54568AN: 151952Hom.: 10019 Cov.: 32 AF XY: 0.360 AC XY: 26745AN XY: 74270
GnomAD4 genome
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32
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74270
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1455
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
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