chr17-4499242-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001124758.3(SPNS2):c.195G>T(p.Arg65Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,467,300 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000396 AC: 6AN: 151472Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000546 AC: 4AN: 73268Hom.: 0 AF XY: 0.0000472 AC XY: 2AN XY: 42378
GnomAD4 exome AF: 0.000120 AC: 158AN: 1315828Hom.: 0 Cov.: 32 AF XY: 0.000103 AC XY: 67AN XY: 648640
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151472Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 73964
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.195G>T (p.R65S) 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 195, causing the arginine (R) at amino acid position 65 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