17-4499258-C-CCCCCCGGCA
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001124758.3(SPNS2):c.229_237dupACCCCCGGC(p.Thr77_Gly79dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000965 in 1,461,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001124758.3 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPNS2 | NM_001124758.3 | c.229_237dupACCCCCGGC | p.Thr77_Gly79dup | conservative_inframe_insertion | Exon 1 of 13 | ENST00000329078.8 | NP_001118230.1 | |
SPNS2 | XR_007065260.1 | n.396_404dupACCCCCGGC | non_coding_transcript_exon_variant | Exon 1 of 13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPNS2 | ENST00000329078.8 | c.229_237dupACCCCCGGC | p.Thr77_Gly79dup | conservative_inframe_insertion | Exon 1 of 13 | 1 | NM_001124758.3 | ENSP00000333292.3 | ||
SPNS2-AS1 | ENST00000416958.1 | n.48+360_48+368dupTGCCGGGGG | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000185 AC: 28AN: 151440Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000684 AC: 5AN: 73108Hom.: 0 AF XY: 0.0000950 AC XY: 4AN XY: 42088
GnomAD4 exome AF: 0.0000863 AC: 113AN: 1309942Hom.: 0 Cov.: 32 AF XY: 0.0000930 AC XY: 60AN XY: 645264
GnomAD4 genome AF: 0.000185 AC: 28AN: 151542Hom.: 0 Cov.: 32 AF XY: 0.000297 AC XY: 22AN XY: 74018
ClinVar
Submissions by phenotype
SPNS2-related disorder Uncertain:1
The SPNS2 c.229_237dup9 variant is predicted to result in an in-frame duplication (p.Thr77_Gly79dup). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.074% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at