rs3824789
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003061.3(SLIT1):c.2165-222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,932 control chromosomes in the GnomAD database, including 10,022 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 0.35 ( 10022 hom., cov: 31)
Consequence
SLIT1
NM_003061.3 intron
NM_003061.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0250
Genes affected
SLIT1 (HGNC:11085): (slit guidance ligand 1) Enables Roundabout binding activity. Involved in axon extension involved in axon guidance; motor neuron axon guidance; and negative chemotaxis. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLIT1 | NM_003061.3 | c.2165-222C>T | intron_variant | ENST00000266058.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLIT1 | ENST00000266058.9 | c.2165-222C>T | intron_variant | 1 | NM_003061.3 | P1 | |||
SLIT1 | ENST00000314867.9 | c.2144-222C>T | intron_variant | 5 | |||||
SLIT1 | ENST00000371070.8 | c.2165-222C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.350 AC: 53121AN: 151814Hom.: 10008 Cov.: 31
GnomAD3 genomes
?
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151814
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.350 AC: 53185AN: 151932Hom.: 10022 Cov.: 31 AF XY: 0.344 AC XY: 25530AN XY: 74266
GnomAD4 genome
?
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53185
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151932
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31
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25530
AN XY:
74266
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Asia WGS
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1057
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3478
ClinVar
Not reported inComputational scores
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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