chr8-42732433-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000749.5(CHRNB3):āc.1126A>Cā(p.Lys376Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000749.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB3 | NM_000749.5 | c.1126A>C | p.Lys376Gln | missense_variant | 5/6 | ENST00000289957.3 | |
CHRNB3 | NM_001347717.2 | c.904A>C | p.Lys302Gln | missense_variant | 6/7 | ||
CHRNB3 | XM_011544390.3 | c.739A>C | p.Lys247Gln | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB3 | ENST00000289957.3 | c.1126A>C | p.Lys376Gln | missense_variant | 5/6 | 1 | NM_000749.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250986Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135712
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727220
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.1126A>C (p.K376Q) alteration is located in exon 5 (coding exon 5) of the CHRNB3 gene. This alteration results from a A to C substitution at nucleotide position 1126, causing the lysine (K) at amino acid position 376 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at