GeneBe

rs761361955

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000080.4(CHRNE):​c.1033-8_1033-3delTGCCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000724 in 1,381,788 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

CHRNE
NM_000080.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.54

Publications

0 publications found
Variant links:
Genes affected
CHRNE (HGNC:1966): (cholinergic receptor nicotinic epsilon subunit) Acetylcholine receptors at mature mammalian neuromuscular junctions are pentameric protein complexes composed of four subunits in the ratio of two alpha subunits to one beta, one epsilon, and one delta subunit. The acetylcholine receptor changes subunit composition shortly after birth when the epsilon subunit replaces the gamma subunit seen in embryonic receptors. Mutations in the epsilon subunit are associated with congenital myasthenic syndrome. [provided by RefSeq, Sep 2009]
C17orf107 (HGNC:37238): (chromosome 17 open reading frame 107)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHRNENM_000080.4 linkc.1033-8_1033-3delTGCCCC splice_region_variant, intron_variant Intron 9 of 11 ENST00000649488.2 NP_000071.1 Q04844
C17orf107NM_001145536.2 linkc.-376_-371delGGGGCA upstream_gene_variant ENST00000381365.4 NP_001139008.1 Q6ZR85

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHRNEENST00000649488.2 linkc.1033-8_1033-3delTGCCCC splice_region_variant, intron_variant Intron 9 of 11 NM_000080.4 ENSP00000497829.1 Q04844
C17orf107ENST00000381365.4 linkc.-376_-371delGGGGCA upstream_gene_variant 2 NM_001145536.2 ENSP00000370770.3 Q6ZR85

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.24e-7
AC:
1
AN:
1381788
Hom.:
0
AF XY:
0.00000147
AC XY:
1
AN XY:
681866
show subpopulations
African (AFR)
AF:
0.0000320
AC:
1
AN:
31250
American (AMR)
AF:
0.00
AC:
0
AN:
33698
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24408
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35886
South Asian (SAS)
AF:
0.00
AC:
0
AN:
78848
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
39382
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4708
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1076248
Other (OTH)
AF:
0.00
AC:
0
AN:
57360
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs761361955; hg19: chr17-4802681; API