16-68370934-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018667.4(SMPD3):c.1248G>A(p.Met416Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000209 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251112Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135782
GnomAD4 exome AF: 0.000221 AC: 323AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.000221 AC XY: 161AN XY: 727218
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1248G>A (p.M416I) 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 1248, causing the methionine (M) at amino acid position 416 to be replaced by an isoleucine (I). 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