chr17-4531050-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001124758.3(SPNS2):c.726-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 1,613,880 control chromosomes in the GnomAD database, including 541 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001124758.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPNS2 | NM_001124758.3 | c.726-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000329078.8 | |||
SPNS2 | XM_047435339.1 | c.273-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SPNS2 | XR_007065260.1 | n.893-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
SPNS2 | XR_007065261.1 | n.563-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPNS2 | ENST00000329078.8 | c.726-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001124758.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0192 AC: 2922AN: 152222Hom.: 29 Cov.: 33
GnomAD3 exomes AF: 0.0202 AC: 5007AN: 248306Hom.: 69 AF XY: 0.0208 AC XY: 2806AN XY: 135004
GnomAD4 exome AF: 0.0256 AC: 37398AN: 1461540Hom.: 512 Cov.: 32 AF XY: 0.0254 AC XY: 18455AN XY: 727072
GnomAD4 genome ? AF: 0.0192 AC: 2922AN: 152340Hom.: 29 Cov.: 33 AF XY: 0.0187 AC XY: 1395AN XY: 74482
ClinVar
Submissions by phenotype
SPNS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 16, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at