15-32691753-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001144757.3(SCG5):c.533G>A(p.Arg178Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,612,364 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 (★).
Frequency
Consequence
NM_001144757.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCG5 | NM_001144757.3 | c.533G>A | p.Arg178Gln | missense_variant | Exon 5 of 6 | ENST00000300175.9 | NP_001138229.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCG5 | ENST00000300175.9 | c.533G>A | p.Arg178Gln | missense_variant | Exon 5 of 6 | 1 | NM_001144757.3 | ENSP00000300175.4 | ||
ARHGAP11A-SCG5 | ENST00000692248.1 | c.1772G>A | p.Arg591Gln | missense_variant | Exon 13 of 14 | ENSP00000510771.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246488Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133678
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460166Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726190
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.533G>A (p.R178Q) alteration is located in exon 5 (coding exon 4) of the SCG5 gene. This alteration results from a G to A substitution at nucleotide position 533, causing the arginine (R) at amino acid position 178 to be replaced by a glutamine (Q). 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