15-41850928-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016642.4(SPTBN5):c.10847G>A(p.Gly3616Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G3616R) has been classified as Uncertain significance.
Frequency
Consequence
NM_016642.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPTBN5 | NM_016642.4 | c.10847G>A | p.Gly3616Glu | missense_variant | Exon 66 of 68 | ENST00000320955.8 | NP_057726.4 | |
SPTBN5 | XM_017022299.2 | c.11027G>A | p.Gly3676Glu | missense_variant | Exon 64 of 66 | XP_016877788.1 | ||
SPTBN5 | XM_017022302.2 | c.8204G>A | p.Gly2735Glu | missense_variant | Exon 52 of 54 | XP_016877791.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.10742G>A (p.G3581E) alteration is located in exon 66 (coding exon 65) of the SPTBN5 gene. This alteration results from a G to A substitution at nucleotide position 10742, causing the glycine (G) at amino acid position 3581 to be replaced by a glutamic acid (E). 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
Publications
No publications associated with this variant yet.