rs199699339
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PP3_StrongBP6BS2
The NM_000744.7(CHRNA4):c.254C>T(p.Thr85Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000749 in 1,601,270 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. T85T) has been classified as Likely benign.
Frequency
Consequence
NM_000744.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.254C>T | p.Thr85Met | missense_variant | 3/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.-293C>T | 5_prime_UTR_variant | 3/6 | |||
CHRNA4 | NR_046317.2 | n.438C>T | non_coding_transcript_exon_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.254C>T | p.Thr85Met | missense_variant | 3/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 229420Hom.: 0 AF XY: 0.0000242 AC XY: 3AN XY: 124036
GnomAD4 exome AF: 0.00000690 AC: 10AN: 1449308Hom.: 0 Cov.: 32 AF XY: 0.00000973 AC XY: 7AN XY: 719484
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74218
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 02, 2020 | Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 22, 2016 | - - |
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at