chr2-130152853-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_017951.5(SMPD4):c.2186G>A(p.Arg729Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000289 in 1,589,684 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R729W) has been classified as Uncertain significance.
Frequency
Consequence
NM_017951.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMPD4 | NM_017951.5 | c.2186G>A | p.Arg729Gln | missense_variant | 20/20 | ENST00000680298.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMPD4 | ENST00000680298.1 | c.2186G>A | p.Arg729Gln | missense_variant | 20/20 | NM_017951.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000301 AC: 7AN: 232638Hom.: 0 AF XY: 0.0000319 AC XY: 4AN XY: 125518
GnomAD4 exome AF: 0.0000292 AC: 42AN: 1437528Hom.: 0 Cov.: 31 AF XY: 0.0000253 AC XY: 18AN XY: 711916
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2022 | The c.2303G>A (p.R768Q) alteration is located in exon 20 (coding exon 20) of the SMPD4 gene. This alteration results from a G to A substitution at nucleotide position 2303, causing the arginine (R) at amino acid position 768 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