chr17-7445115-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000747.3(CHRNB1):c.-13G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000509 in 1,606,214 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000747.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNB1 | ENST00000306071 | c.-13G>C | 5_prime_UTR_variant | Exon 1 of 11 | 1 | NM_000747.3 | ENSP00000304290.2 | |||
ENSG00000272884 | ENST00000575331.1 | n.4702G>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
CHRNB1 | ENST00000572857 | c.-13G>C | 5_prime_UTR_variant | Exon 1 of 6 | 4 | ENSP00000461402.1 | ||||
CHRNB1 | ENST00000574054.1 | n.8G>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00262 AC: 398AN: 152168Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000721 AC: 165AN: 228986Hom.: 0 AF XY: 0.000559 AC XY: 71AN XY: 126990
GnomAD4 exome AF: 0.000288 AC: 419AN: 1453930Hom.: 1 Cov.: 31 AF XY: 0.000213 AC XY: 154AN XY: 723236
GnomAD4 genome AF: 0.00261 AC: 398AN: 152284Hom.: 3 Cov.: 33 AF XY: 0.00265 AC XY: 197AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
CHRNB1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Congenital myasthenic syndrome 4C Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at