6-109443360-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003080.3(SMPD2):c.823C>A(p.Leu275Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,984 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_003080.3 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 |
---|---|---|---|---|---|---|---|---|
SMPD2 | NM_003080.3 | c.823C>A | p.Leu275Met | missense_variant | Exon 9 of 10 | ENST00000258052.8 | NP_003071.2 | |
SMPD2 | XM_011536079.2 | c.508C>A | p.Leu170Met | missense_variant | Exon 7 of 8 | XP_011534381.1 | ||
SMPD2 | XR_942566.3 | n.1156C>A | non_coding_transcript_exon_variant | Exon 9 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251454Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135920
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461774Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 727200
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.823C>A (p.L275M) alteration is located in exon 9 (coding exon 9) of the SMPD2 gene. This alteration results from a C to A substitution at nucleotide position 823, causing the leucine (L) at amino acid position 275 to be replaced by a methionine (M). 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