17-4499168-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001124758.3(SPNS2):c.121G>T(p.Gly41Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000667 in 149,884 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_001124758.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000667 AC: 1AN: 149884Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000186 AC: 2AN: 1075110Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 512542
GnomAD4 genome AF: 0.00000667 AC: 1AN: 149884Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73100
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.121G>T (p.G41W) alteration is located in exon 1 (coding exon 1) of the SPNS2 gene. This alteration results from a G to T substitution at nucleotide position 121, causing the glycine (G) at amino acid position 41 to be replaced by a tryptophan (W). 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