rs45588436
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000744.7(CHRNA4):c.681C>T(p.Ala227=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. A227A) has been classified as Likely benign.
Frequency
Consequence
NM_000744.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.681C>T | p.Ala227= | synonymous_variant | 5/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.153C>T | p.Ala51= | synonymous_variant | 5/6 | ||
CHRNA4 | NR_046317.2 | n.890C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.681C>T | p.Ala227= | synonymous_variant | 5/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151806Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250924Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135790
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461684Hom.: 0 Cov.: 99 AF XY: 0.0000261 AC XY: 19AN XY: 727114
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151806Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74112
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at