chr2-151603754-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001164507.2(NEB):āc.13078C>Gā(p.Leu4360Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L4360L) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
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.13078C>G | p.Leu4360Val | missense_variant | 86/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.13078C>G | p.Leu4360Val | missense_variant | 86/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.13078C>G | p.Leu4360Val | missense_variant | 86/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.13078C>G | p.Leu4360Val | missense_variant | 86/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.11601+6055C>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 152AN: 151852Hom.: 1 Cov.: 22 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000852 AC: 119AN: 1397390Hom.: 0 Cov.: 32 AF XY: 0.0000711 AC XY: 49AN XY: 689230
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00100 AC: 152AN: 151970Hom.: 1 Cov.: 22 AF XY: 0.000968 AC XY: 72AN XY: 74344
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 23, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at