16-68371005-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018667.4(SMPD3):c.1177G>A(p.Gly393Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000774 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018667.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251150Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135820
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727212
GnomAD4 genome AF: 0.000302 AC: 46AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1177G>A (p.G393S) alteration is located in exon 3 (coding exon 1) of the SMPD3 gene. This alteration results from a G to A substitution at nucleotide position 1177, causing the glycine (G) at amino acid position 393 to be replaced by a serine (S). 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