12-120810884-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139015.5(SPPL3):c.26C>T(p.Ala9Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,611,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_139015.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPPL3 | NM_139015.5 | c.26C>T | p.Ala9Val | missense_variant, splice_region_variant | Exon 2 of 11 | ENST00000353487.7 | NP_620584.2 | |
SPPL3 | XM_011537925.3 | c.26C>T | p.Ala9Val | missense_variant, splice_region_variant | Exon 2 of 11 | XP_011536227.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250932Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135686
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1459750Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726352
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.26C>T (p.A9V) alteration is located in exon 2 (coding exon 2) of the SPPL3 gene. This alteration results from a C to T substitution at nucleotide position 26, causing the alanine (A) at amino acid position 9 to be replaced by a valine (V). 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