rs1553877868
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001164507.2(NEB):c.12406G>A(p.Val4136Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V4136G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.12406G>A | p.Val4136Met | missense_variant | 82/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.12406G>A | p.Val4136Met | missense_variant | 82/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.12406G>A | p.Val4136Met | missense_variant | 82/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.12406G>A | p.Val4136Met | missense_variant | 82/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.11601+1208G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 4
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 4
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jul 12, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at