4-20253683-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004787.4(SLIT2):c.-133G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 995,306 control chromosomes in the GnomAD database, including 275,688 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
Consequence
NM_004787.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLIT2 | ENST00000504154 | c.-133G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 37 | 1 | NM_004787.4 | ENSP00000422591.1 | |||
SLIT2 | ENST00000504154 | c.-133G>T | 5_prime_UTR_variant | Exon 1 of 37 | 1 | NM_004787.4 | ENSP00000422591.1 |
Frequencies
GnomAD3 genomes AF: 0.766 AC: 116347AN: 151804Hom.: 44898 Cov.: 30
GnomAD4 exome AF: 0.736 AC: 620962AN: 843384Hom.: 230760 Cov.: 11 AF XY: 0.737 AC XY: 317703AN XY: 431286
GnomAD4 genome AF: 0.766 AC: 116431AN: 151922Hom.: 44928 Cov.: 30 AF XY: 0.768 AC XY: 57056AN XY: 74262
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at