rs541641039
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001164507.2(NEB):c.5374A>G(p.Lys1792Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000808 in 1,608,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. K1792K) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.5374A>G | p.Lys1792Glu | missense_variant | 44/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.5374A>G | p.Lys1792Glu | missense_variant | 44/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.5374A>G | p.Lys1792Glu | missense_variant | 44/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.5374A>G | p.Lys1792Glu | missense_variant | 44/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.5374A>G | p.Lys1792Glu | missense_variant | 44/150 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000378 AC: 9AN: 238076Hom.: 0 AF XY: 0.0000466 AC XY: 6AN XY: 128882
GnomAD4 exome AF: 0.00000755 AC: 11AN: 1456038Hom.: 0 Cov.: 30 AF XY: 0.00000691 AC XY: 5AN XY: 723620
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74506
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at