chr10-97002344-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_003061.3(SLIT1):c.4180C>T(p.Leu1394Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,609,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L1394L) has been classified as Likely benign.
Frequency
Consequence
NM_003061.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLIT1 | NM_003061.3 | c.4180C>T | p.Leu1394Phe | missense_variant | 36/37 | ENST00000266058.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLIT1 | ENST00000266058.9 | c.4180C>T | p.Leu1394Phe | missense_variant | 36/37 | 1 | NM_003061.3 | P1 | |
SLIT1 | ENST00000371070.8 | c.4180C>T | p.Leu1394Phe | missense_variant | 36/37 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457084Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 724706
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | The c.4180C>T (p.L1394F) alteration is located in exon 36 (coding exon 36) of the SLIT1 gene. This alteration results from a C to T substitution at nucleotide position 4180, causing the leucine (L) at amino acid position 1394 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at