rs1057521174
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_001164507.2(NEB):c.13370A>C(p.Lys4457Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001164507.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.13370A>C | p.Lys4457Thr | missense_variant, splice_region_variant | 88/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.13370A>C | p.Lys4457Thr | missense_variant, splice_region_variant | 88/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.13370A>C | p.Lys4457Thr | missense_variant, splice_region_variant | 88/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.13370A>C | p.Lys4457Thr | missense_variant, splice_region_variant | 88/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.11601+7802A>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD4 exome Cov.: 0
GnomAD4 genome ? Cov.: 0
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2017 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 24, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at