16-68361685-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018667.4(SMPD3):c.1784G>A(p.Arg595Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,612,714 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. R595W) has been classified as Uncertain significance.
Frequency
Consequence
NM_018667.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250696Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135662
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460510Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726598
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1784G>A (p.R595Q) alteration is located in exon 8 (coding exon 6) of the SMPD3 gene. This alteration results from a G to A substitution at nucleotide position 1784, causing the arginine (R) at amino acid position 595 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