rs200527878
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP3BP6_ModerateBS2
The NM_000744.7(CHRNA4):c.211G>A(p.Ala71Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,612,708 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A71V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000744.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.211G>A | p.Ala71Thr | missense_variant | 2/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.-336G>A | 5_prime_UTR_variant | 2/6 | |||
CHRNA4 | NR_046317.2 | n.395G>A | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.211G>A | p.Ala71Thr | missense_variant | 2/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249820Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135626
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460368Hom.: 0 Cov.: 38 AF XY: 0.0000124 AC XY: 9AN XY: 726476
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152340Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74492
ClinVar
Submissions by phenotype
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at