1-154571362-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_000748.3(CHRNB2):c.539G>T(p.Arg180Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R180C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000748.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNB2 | NM_000748.3 | c.539G>T | p.Arg180Leu | missense_variant | Exon 5 of 6 | ENST00000368476.4 | NP_000739.1 | |
CHRNB2 | XM_017000180.3 | c.29G>T | p.Arg10Leu | missense_variant | Exon 2 of 3 | XP_016855669.1 | ||
CHRNB2 | XR_001736952.3 | n.806G>T | non_coding_transcript_exon_variant | Exon 5 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNB2 | ENST00000368476.4 | c.539G>T | p.Arg180Leu | missense_variant | Exon 5 of 6 | 1 | NM_000748.3 | ENSP00000357461.3 | ||
CHRNB2 | ENST00000637900.1 | c.545G>T | p.Arg182Leu | missense_variant | Exon 5 of 6 | 5 | ENSP00000490474.1 | |||
CHRNB2 | ENST00000636034.1 | n.539G>T | non_coding_transcript_exon_variant | Exon 5 of 9 | 5 | ENSP00000489703.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
CHRNB2-related disorder Uncertain:1
The CHRNB2 c.539G>T variant is predicted to result in the amino acid substitution p.Arg180Leu. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.