NM_000747.3:c.40_48delGGGGCGCCG
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4
The NM_000747.3(CHRNB1):c.40_48delGGGGCGCCG(p.Gly14_Pro16del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000311 in 1,609,238 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000034 ( 0 hom. )
Consequence
CHRNB1
NM_000747.3 conservative_inframe_deletion
NM_000747.3 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.07
Publications
0 publications found
Genes affected
CHRNB1 (HGNC:1961): (cholinergic receptor nicotinic beta 1 subunit) The muscle acetylcholine receptor is composed of five subunits: two alpha subunits and one beta, one gamma, and one delta subunit. This gene encodes the beta subunit of the acetylcholine receptor. The acetylcholine receptor changes conformation upon acetylcholine binding leading to the opening of an ion-conducting channel across the plasma membrane. Mutations in this gene are associated with slow-channel congenital myasthenic syndrome. [provided by RefSeq, Jul 2008]
ENSG00000272884 (HGNC:):
FGF11 (HGNC:3667): (fibroblast growth factor 11) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. The function of this gene has not yet been determined. The expression pattern of the mouse homolog implies a role in nervous system development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_000747.3.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000747.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHRNB1 | MANE Select | c.40_48delGGGGCGCCG | p.Gly14_Pro16del | conservative_inframe_deletion | Exon 1 of 11 | NP_000738.2 | |||
| FGF11 | MANE Select | c.*2020_*2028delGGGGGCGCC | downstream_gene | N/A | NP_004103.1 | Q92914 | |||
| FGF11 | c.*2020_*2028delGGGGGCGCC | downstream_gene | N/A | NP_001290389.1 | B7Z1C3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHRNB1 | TSL:1 MANE Select | c.40_48delGGGGCGCCG | p.Gly14_Pro16del | conservative_inframe_deletion | Exon 1 of 11 | ENSP00000304290.2 | P11230-1 | ||
| ENSG00000272884 | TSL:1 | n.4754_4762delGGGGCGCCG | non_coding_transcript_exon | Exon 3 of 3 | |||||
| CHRNB1 | TSL:4 | c.40_48delGGGGCGCCG | p.Gly14_Pro16del | conservative_inframe_deletion | Exon 1 of 6 | ENSP00000461402.1 | I3L4N5 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 151954Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151954
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: 0.0000336 AC: 49AN: 1457284Hom.: 0 AF XY: 0.0000317 AC XY: 23AN XY: 724930 show subpopulations
GnomAD4 exome
AF:
AC:
49
AN:
1457284
Hom.:
AF XY:
AC XY:
23
AN XY:
724930
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33432
American (AMR)
AF:
AC:
0
AN:
44604
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26068
East Asian (EAS)
AF:
AC:
0
AN:
39666
South Asian (SAS)
AF:
AC:
0
AN:
86104
European-Finnish (FIN)
AF:
AC:
0
AN:
50626
Middle Eastern (MID)
AF:
AC:
2
AN:
5226
European-Non Finnish (NFE)
AF:
AC:
45
AN:
1111394
Other (OTH)
AF:
AC:
2
AN:
60164
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.431
Heterozygous variant carriers
0
3
7
10
14
17
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000658 AC: 1AN: 151954Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74228 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151954
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74228
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41380
American (AMR)
AF:
AC:
0
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5154
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10582
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67964
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
1
-
Congenital myasthenic syndrome 2A (1)
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.