15-51688400-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013243.4(SCG3):c.538C>T(p.Leu180Phe) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000881 in 1,612,548 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013243.4 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCG3 | NM_013243.4 | c.538C>T | p.Leu180Phe | missense_variant, splice_region_variant | Exon 5 of 12 | ENST00000220478.8 | NP_037375.2 | |
SCG3 | NM_001165257.2 | c.-159C>T | splice_region_variant | Exon 4 of 11 | NP_001158729.1 | |||
SCG3 | NM_001165257.2 | c.-159C>T | 5_prime_UTR_variant | Exon 4 of 11 | NP_001158729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCG3 | ENST00000220478.8 | c.538C>T | p.Leu180Phe | missense_variant, splice_region_variant | Exon 5 of 12 | 1 | NM_013243.4 | ENSP00000220478.3 | ||
SCG3 | ENST00000542355.6 | c.-159C>T | splice_region_variant | Exon 4 of 11 | 2 | ENSP00000445205.2 | ||||
SCG3 | ENST00000542355 | c.-159C>T | 5_prime_UTR_variant | Exon 4 of 11 | 2 | ENSP00000445205.2 | ||||
SCG3 | ENST00000558709.1 | c.-156-819C>T | intron_variant | Intron 3 of 4 | 2 | ENSP00000452745.1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000144 AC: 36AN: 250514Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135434
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1460414Hom.: 0 Cov.: 30 AF XY: 0.0000812 AC XY: 59AN XY: 726422
GnomAD4 genome AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.538C>T (p.L180F) alteration is located in exon 5 (coding exon 5) of the SCG3 gene. This alteration results from a C to T substitution at nucleotide position 538, causing the leucine (L) at amino acid position 180 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