rs56000199
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_000744.7(CHRNA4):c.1661C>T(p.Pro554Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,612,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P554P) has been classified as Likely benign.
Frequency
Consequence
NM_000744.7 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 |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.1661C>T | p.Pro554Leu | missense_variant | 5/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.1133C>T | p.Pro378Leu | missense_variant | 5/6 | ||
CHRNA4 | NR_046317.2 | n.1870C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.1661C>T | p.Pro554Leu | missense_variant | 5/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152232Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.0000766 AC: 19AN: 247938Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134746
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1459824Hom.: 0 Cov.: 34 AF XY: 0.0000496 AC XY: 36AN XY: 726146
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152350Hom.: 1 Cov.: 34 AF XY: 0.0000671 AC XY: 5AN XY: 74508
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at