14-63686184-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_030791.4(SGPP1):c.1247G>A(p.Arg416Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,613,450 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030791.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 151922Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251116Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135722
GnomAD4 exome AF: 0.000179 AC: 261AN: 1461528Hom.: 0 Cov.: 31 AF XY: 0.000177 AC XY: 129AN XY: 727060
GnomAD4 genome AF: 0.000118 AC: 18AN: 151922Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74160
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1247G>A (p.R416Q) alteration is located in exon 3 (coding exon 3) of the SGPP1 gene. This alteration results from a G to A substitution at nucleotide position 1247, causing the arginine (R) at amino acid position 416 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