2-232539880-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
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
Publications
8 publications found
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]
CHRNG Gene-Disease associations (from GenCC):
- autosomal recessive multiple pterygium syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Orphanet
- CHRNG-associated hypo-akinesia disorder of prenatal onsetInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- lethal multiple pterygium syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Orphanet
- transient neonatal myasthenia gravisInheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 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_multiple_submitters_no_conflicts, 2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNG | NM_005199.5 | c.55+78G>C | intron_variant | Intron 1 of 11 | ENST00000651502.1 | NP_005190.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNG | ENST00000651502.1 | c.55+78G>C | intron_variant | Intron 1 of 11 | NM_005199.5 | ENSP00000498757.1 | ||||
CHRNG | ENST00000389492.3 | c.55+78G>C | intron_variant | Intron 1 of 10 | 1 | ENSP00000374143.3 | ||||
CHRNG | ENST00000485094.1 | n.76+78G>C | intron_variant | Intron 1 of 4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.310 AC: 47073AN: 151940Hom.: 7988 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
47073
AN:
151940
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.349 AC: 507960AN: 1456410Hom.: 91225 Cov.: 33 AF XY: 0.350 AC XY: 253833AN XY: 724526 show subpopulations
GnomAD4 exome
AF:
AC:
507960
AN:
1456410
Hom.:
Cov.:
33
AF XY:
AC XY:
253833
AN XY:
724526
show subpopulations
African (AFR)
AF:
AC:
5589
AN:
33350
American (AMR)
AF:
AC:
24307
AN:
44650
Ashkenazi Jewish (ASJ)
AF:
AC:
9718
AN:
26078
East Asian (EAS)
AF:
AC:
17630
AN:
39662
South Asian (SAS)
AF:
AC:
35073
AN:
86128
European-Finnish (FIN)
AF:
AC:
16100
AN:
53106
Middle Eastern (MID)
AF:
AC:
1580
AN:
4834
European-Non Finnish (NFE)
AF:
AC:
377264
AN:
1108470
Other (OTH)
AF:
AC:
20699
AN:
60132
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
18395
36789
55184
73578
91973
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.310 AC: 47109AN: 152058Hom.: 8006 Cov.: 33 AF XY: 0.313 AC XY: 23251AN XY: 74316 show subpopulations
GnomAD4 genome
AF:
AC:
47109
AN:
152058
Hom.:
Cov.:
33
AF XY:
AC XY:
23251
AN XY:
74316
show subpopulations
African (AFR)
AF:
AC:
7505
AN:
41514
American (AMR)
AF:
AC:
6809
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1257
AN:
3468
East Asian (EAS)
AF:
AC:
2289
AN:
5158
South Asian (SAS)
AF:
AC:
1950
AN:
4812
European-Finnish (FIN)
AF:
AC:
3145
AN:
10584
Middle Eastern (MID)
AF:
AC:
101
AN:
294
European-Non Finnish (NFE)
AF:
AC:
23003
AN:
67926
Other (OTH)
AF:
AC:
685
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1651
3303
4954
6606
8257
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1607
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Oct 02, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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