chr5-168666648-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003062.4(SLIT3):c.4378C>T(p.Arg1460Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000675 in 1,614,050 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1460H) has been classified as Benign.
Frequency
Consequence
NM_003062.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLIT3 | NM_003062.4 | c.4378C>T | p.Arg1460Cys | missense_variant | 36/36 | ENST00000519560.6 | |
SLIT3 | NM_001271946.2 | c.4399C>T | p.Arg1467Cys | missense_variant | 36/36 | ||
SLIT3 | XM_017009779.1 | c.4189C>T | p.Arg1397Cys | missense_variant | 36/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLIT3 | ENST00000519560.6 | c.4378C>T | p.Arg1460Cys | missense_variant | 36/36 | 1 | NM_003062.4 | A1 | |
SLIT3 | ENST00000332966.8 | c.4399C>T | p.Arg1467Cys | missense_variant | 36/36 | 1 | P4 | ||
ENST00000520041.1 | n.536G>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000100 AC: 25AN: 249100Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134840
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 727236
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2023 | The c.4378C>T (p.R1460C) alteration is located in exon 36 (coding exon 36) of the SLIT3 gene. This alteration results from a C to T substitution at nucleotide position 4378, causing the arginine (R) at amino acid position 1460 to be replaced by a cysteine (C). 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