rs1553867144
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001164507.2(NEB):c.13218C>T(p.Thr4406=) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T4406T) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.13218C>T | p.Thr4406= | synonymous_variant | 86/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.13218C>T | p.Thr4406= | synonymous_variant | 86/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.13218C>T | p.Thr4406= | synonymous_variant | 86/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.13218C>T | p.Thr4406= | synonymous_variant | 86/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.11601+6195C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 21
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 20, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.