rs201434993
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM1BP4_Moderate
The NM_000080.4(CHRNE):c.710G>T(p.Arg237Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000992 in 1,613,702 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R237C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000080.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNE | NM_000080.4 | c.710G>T | p.Arg237Leu | missense_variant | 7/12 | ENST00000649488.2 | |
C17orf107 | NM_001145536.2 | c.*549C>A | 3_prime_UTR_variant | 3/3 | ENST00000381365.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNE | ENST00000649488.2 | c.710G>T | p.Arg237Leu | missense_variant | 7/12 | NM_000080.4 | P1 | ||
C17orf107 | ENST00000381365.4 | c.*549C>A | 3_prime_UTR_variant | 3/3 | 2 | NM_001145536.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000212 AC: 53AN: 249946Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 135214
GnomAD4 exome AF: 0.000101 AC: 148AN: 1461554Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 78AN XY: 727102
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74322
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 4A Pathogenic:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 07, 2018 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 07, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2018 | - - |
Congenital myasthenic syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 05, 2020 | - - |
Congenital myasthenic syndrome 4C;C4225369:Congenital myasthenic syndrome 4B;C4225413:Congenital myasthenic syndrome 4A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jun 05, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at