chr17-7445153-TGCTGGGGGC-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_000747.3(CHRNB1):c.38_46delTGGGGGCGC(p.Leu13_Ala15del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,609,634 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000747.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNB1 | ENST00000306071.7 | c.38_46delTGGGGGCGC | p.Leu13_Ala15del | disruptive_inframe_deletion | Exon 1 of 11 | 1 | NM_000747.3 | ENSP00000304290.2 | ||
ENSG00000272884 | ENST00000575331.1 | n.4752_4760delTGGGGGCGC | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
CHRNB1 | ENST00000572857.5 | c.38_46delTGGGGGCGC | p.Leu13_Ala15del | disruptive_inframe_deletion | Exon 1 of 6 | 4 | ENSP00000461402.1 | |||
CHRNB1 | ENST00000574054.1 | n.58_66delTGGGGGCGC | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000170 AC: 4AN: 235750Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 130138
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1457420Hom.: 0 AF XY: 0.0000221 AC XY: 16AN XY: 724994
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 2A Uncertain:1
This variant, c.38_46del, results in the deletion of 3 amino acid(s) of the CHRNB1 protein (p.Leu13_Ala15del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs754981832, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with CHRNB1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at