2-54612329-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP2PP3_Strong
The NM_003128.3(SPTBN1):c.469T>G(p.Phe157Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003128.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN1 | NM_003128.3 | c.469T>G | p.Phe157Val | missense_variant | 4/36 | ENST00000356805.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN1 | ENST00000356805.9 | c.469T>G | p.Phe157Val | missense_variant | 4/36 | 1 | NM_003128.3 | P1 | |
SPTBN1 | ENST00000333896.5 | c.430T>G | p.Phe144Val | missense_variant | 3/31 | 1 | |||
SPTBN1 | ENST00000389980.7 | c.469T>G | p.Phe157Val | missense_variant | 4/14 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Developmental delay, impaired speech, and behavioral abnormalities Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Bruce Lefroy Centre, Murdoch Childrens Research Institute | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.