rs200810080
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_000744.7(CHRNA4):c.1697G>A(p.Arg566Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R566W) has been classified as Uncertain significance.
Frequency
Consequence
NM_000744.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.1697G>A | p.Arg566Gln | missense_variant | Exon 5 of 6 | ENST00000370263.9 | NP_000735.1 | |
CHRNA4 | NM_001256573.2 | c.1169G>A | p.Arg390Gln | missense_variant | Exon 5 of 6 | NP_001243502.1 | ||
CHRNA4 | NR_046317.2 | n.1906G>A | non_coding_transcript_exon_variant | Exon 5 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248294Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134982
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460490Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 726576
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy 1 Uncertain:1
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Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at