rs2229961
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000745.4(CHRNA5):c.400G>A(p.Val134Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0146 in 1,501,350 control chromosomes in the GnomAD database, including 219 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000745.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA5 | NM_000745.4 | c.400G>A | p.Val134Ile | missense_variant | 4/6 | ENST00000299565.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA5 | ENST00000299565.9 | c.400G>A | p.Val134Ile | missense_variant | 4/6 | 1 | NM_000745.4 | P1 | |
CHRNA5 | ENST00000394802.4 | c.217G>A | p.Val73Ile | missense_variant | 3/5 | 3 | |||
CHRNA5 | ENST00000559554.5 | c.400G>A | p.Val134Ile | missense_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1563AN: 152150Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.0114 AC: 2450AN: 214324Hom.: 28 AF XY: 0.0127 AC XY: 1477AN XY: 116584
GnomAD4 exome AF: 0.0151 AC: 20364AN: 1349080Hom.: 205 Cov.: 20 AF XY: 0.0151 AC XY: 10098AN XY: 669670
GnomAD4 genome ? AF: 0.0103 AC: 1569AN: 152270Hom.: 14 Cov.: 32 AF XY: 0.0100 AC XY: 746AN XY: 74446
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at