rs768629100
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 1P and 4B. PP2BS2
The NM_003061.3(SLIT1):c.4420T>C(p.Tyr1474His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,460,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003061.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLIT1 | ENST00000266058.9 | c.4420T>C | p.Tyr1474His | missense_variant | Exon 37 of 37 | 1 | NM_003061.3 | ENSP00000266058.4 | ||
SLIT1 | ENST00000371070.8 | c.4296T>C | p.Ala1432Ala | synonymous_variant | Exon 37 of 37 | 5 | ENSP00000360109.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD2 exomes AF: 0.00000400 AC: 1AN: 250016 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1460922Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726776 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4420T>C (p.Y1474H) alteration is located in exon 37 (coding exon 37) of the SLIT1 gene. This alteration results from a T to C substitution at nucleotide position 4420, causing the tyrosine (Y) at amino acid position 1474 to be replaced by a histidine (H). 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