rs56095004
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000750.5(CHRNB4):c.407G>A(p.Arg136Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00792 in 1,610,264 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R136W) has been classified as Likely benign.
Frequency
Consequence
NM_000750.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNB4 | NM_000750.5 | c.407G>A | p.Arg136Gln | missense_variant | 5/6 | ENST00000261751.8 | NP_000741.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNB4 | ENST00000261751.8 | c.407G>A | p.Arg136Gln | missense_variant | 5/6 | 1 | NM_000750.5 | ENSP00000261751.3 | ||
CHRNB4 | ENST00000412074.6 | c.359+1178G>A | intron_variant | 1 | ENSP00000416386.2 | |||||
CHRNB4 | ENST00000559849.5 | n.*463G>A | non_coding_transcript_exon_variant | 12/12 | 1 | ENSP00000457404.1 | ||||
CHRNB4 | ENST00000559849.5 | n.*463G>A | 3_prime_UTR_variant | 12/12 | 1 | ENSP00000457404.1 |
Frequencies
GnomAD3 genomes AF: 0.00539 AC: 820AN: 152018Hom.: 5 Cov.: 31
GnomAD3 exomes AF: 0.00560 AC: 1384AN: 247178Hom.: 7 AF XY: 0.00598 AC XY: 800AN XY: 133768
GnomAD4 exome AF: 0.00818 AC: 11929AN: 1458128Hom.: 55 Cov.: 31 AF XY: 0.00812 AC XY: 5889AN XY: 725248
GnomAD4 genome AF: 0.00539 AC: 820AN: 152136Hom.: 5 Cov.: 31 AF XY: 0.00493 AC XY: 367AN XY: 74384
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at