17-76386915-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001142601.2(SPHK1):c.484C>A(p.Arg162Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,612,726 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142601.2 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: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250724Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135558
GnomAD4 exome AF: 0.000110 AC: 161AN: 1460522Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 726422
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.742C>A (p.R248S) alteration is located in exon 6 (coding exon 6) of the SPHK1 gene. This alteration results from a C to A substitution at nucleotide position 742, causing the arginine (R) at amino acid position 248 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