chr2-54612190-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP2PP3
The NM_003128.3(SPTBN1):c.330C>G(p.Ile110Met) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic 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. I110F) has been classified as Likely benign.
Frequency
Consequence
NM_003128.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN1 | NM_003128.3 | c.330C>G | p.Ile110Met | missense_variant | 4/36 | ENST00000356805.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN1 | ENST00000356805.9 | c.330C>G | p.Ile110Met | missense_variant | 4/36 | 1 | NM_003128.3 | P1 | |
SPTBN1 | ENST00000333896.5 | c.291C>G | p.Ile97Met | missense_variant | 3/31 | 1 | |||
SPTBN1 | ENST00000389980.7 | c.330C>G | p.Ile110Met | missense_variant | 4/14 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | SPTBN1: PM2, PP2, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.