rs139922367
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_000080.4(CHRNE):c.1019C>T(p.Pro340Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,597,414 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P340S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000080.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNE | NM_000080.4 | c.1019C>T | p.Pro340Leu | missense_variant | 9/12 | ENST00000649488.2 | |
CHRNE | XM_017024115.2 | c.983C>T | p.Pro328Leu | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNE | ENST00000649488.2 | c.1019C>T | p.Pro340Leu | missense_variant | 9/12 | NM_000080.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000181 AC: 40AN: 221008Hom.: 0 AF XY: 0.000159 AC XY: 19AN XY: 119722
GnomAD4 exome AF: 0.000172 AC: 249AN: 1445280Hom.: 0 Cov.: 34 AF XY: 0.000170 AC XY: 122AN XY: 717188
GnomAD4 genome AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74304
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 25, 2019 | - - |
Congenital myasthenic syndrome 4A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at