20-63350771-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3BP6BS1BS2
The NM_000744.7(CHRNA4):c.640G>A(p.Ala214Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000236 in 1,613,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A214A) 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 -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.640G>A | p.Ala214Thr | missense_variant | 5/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.112G>A | p.Ala38Thr | missense_variant | 5/6 | ||
CHRNA4 | NR_046317.2 | n.849G>A | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.640G>A | p.Ala214Thr | missense_variant | 5/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151840Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251028Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135842
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461608Hom.: 0 Cov.: 89 AF XY: 0.0000193 AC XY: 14AN XY: 727096
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151840Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74154
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Sep 20, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at