rs1433188091
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_001164507.2(NEB):c.13466T>C(p.Ile4489Thr) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I4489L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.13466T>C | p.Ile4489Thr | missense_variant | 88/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.13466T>C | p.Ile4489Thr | missense_variant | 88/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.13466T>C | p.Ile4489Thr | missense_variant | 88/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.13466T>C | p.Ile4489Thr | missense_variant | 88/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.11601+7898T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 994Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 578
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 08, 2017 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 17, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 04, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at