2-232539880-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005199.5(CHRNG):c.55+78G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 1,608,468 control chromosomes in the GnomAD database, including 99,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.31 ( 8006 hom., cov: 33)
Exomes 𝑓: 0.35 ( 91225 hom. )
Consequence
CHRNG
NM_005199.5 intron
NM_005199.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.59
Genes affected
CHRNG (HGNC:1967): (cholinergic receptor nicotinic gamma subunit) The mammalian muscle-type acetylcholine receptor is a transmembrane pentameric glycoprotein with two alpha subunits, one beta, one delta, and one epsilon (in adult skeletal muscle) or gamma (in fetal and denervated muscle) subunit. This gene, which encodes the gamma subunit, is expressed prior to the thirty-third week of gestation in humans. The gamma subunit of the acetylcholine receptor plays a role in neuromuscular organogenesis and ligand binding and disruption of gamma subunit expression prevents the correct localization of the receptor in cell membranes. Mutations in this gene cause Escobar syndrome and a lethal form of multiple pterygium syndrome. Muscle-type acetylcholine receptor is the major antigen in the autoimmune disease myasthenia gravis.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 2-232539880-G-C is Benign according to our data. Variant chr2-232539880-G-C is described in ClinVar as [Benign]. Clinvar id is 1290181.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNG | NM_005199.5 | c.55+78G>C | intron_variant | ENST00000651502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNG | ENST00000651502.1 | c.55+78G>C | intron_variant | NM_005199.5 | P1 | ||||
CHRNG | ENST00000389492.3 | c.55+78G>C | intron_variant | 1 | |||||
CHRNG | ENST00000485094.1 | n.76+78G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.310 AC: 47073AN: 151940Hom.: 7988 Cov.: 33
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GnomAD4 exome AF: 0.349 AC: 507960AN: 1456410Hom.: 91225 Cov.: 33 AF XY: 0.350 AC XY: 253833AN XY: 724526
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GnomAD4 genome ? AF: 0.310 AC: 47109AN: 152058Hom.: 8006 Cov.: 33 AF XY: 0.313 AC XY: 23251AN XY: 74316
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 02, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at