rs1159106476
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_000080.4(CHRNE):c.1179C>T(p.Leu393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000055 in 1,454,884 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L393L) has been classified as Likely benign.
Frequency
Consequence
NM_000080.4 synonymous
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 |
---|---|---|---|---|---|---|---|
CHRNE | NM_000080.4 | c.1179C>T | p.Leu393= | synonymous_variant | 10/12 | ENST00000649488.2 | |
CHRNE | XM_017024115.2 | c.1143C>T | p.Leu381= | synonymous_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNE | ENST00000649488.2 | c.1179C>T | p.Leu393= | synonymous_variant | 10/12 | NM_000080.4 | P1 | ||
CHRNE | ENST00000649830.1 | c.246C>T | p.Leu82= | synonymous_variant | 10/11 | ||||
CHRNE | ENST00000572438.1 | n.865C>T | non_coding_transcript_exon_variant | 5/7 | 5 | ||||
CHRNE | ENST00000652550.1 | n.909C>T | non_coding_transcript_exon_variant | 2/4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237568Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130398
GnomAD4 exome AF: 0.00000550 AC: 8AN: 1454884Hom.: 0 Cov.: 35 AF XY: 0.00000414 AC XY: 3AN XY: 723938
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 4A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at