rs121912257
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000744.7(CHRNA4):c.858C>T(p.Thr286=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,613,770 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. T286T) 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 -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.858C>T | p.Thr286= | synonymous_variant | 5/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.330C>T | p.Thr110= | synonymous_variant | 5/6 | ||
CHRNA4 | NR_046317.2 | n.1067C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.858C>T | p.Thr286= | synonymous_variant | 5/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251026Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135838
GnomAD4 exome AF: 0.0000581 AC: 85AN: 1461768Hom.: 0 Cov.: 99 AF XY: 0.0000536 AC XY: 39AN XY: 727162
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74234
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 25, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2020 | - - |
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2023 | - - |
Tobacco use disorder Other:1
not provided, no classification provided | literature only | Psychiatry Genetics Yale University | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at