rs1057515574
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001164507.2(NEB):c.23398_23399insGTTT(p.Leu7800CysfsTer25) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,164 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L7800L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001164507.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.23398_23399insGTTT | p.Leu7800CysfsTer25 | frameshift_variant | 162/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.23398_23399insGTTT | p.Leu7800CysfsTer25 | frameshift_variant | 162/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.23398_23399insGTTT | p.Leu7800CysfsTer25 | frameshift_variant | 162/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.23398_23399insGTTT | p.Leu7800CysfsTer25 | frameshift_variant | 162/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244476Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132550
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458942Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 725474
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 02, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at