rs6089898
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_000744.7(CHRNA4):āc.24G>Cā(p.Ala8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,476,610 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign 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. A8A) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.24G>C | p.Ala8= | synonymous_variant | 1/6 | ENST00000370263.9 | |
LOC100130587 | NR_110634.1 | n.183-676C>G | intron_variant, non_coding_transcript_variant | ||||
CHRNA4 | NM_001256573.2 | c.-471+35G>C | intron_variant | ||||
CHRNA4 | NR_046317.2 | n.208G>C | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.24G>C | p.Ala8= | synonymous_variant | 1/6 | 1 | NM_000744.7 | P1 | |
ENST00000370257.1 | n.183-676C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00840 AC: 1273AN: 151558Hom.: 24 Cov.: 31
GnomAD3 exomes AF: 0.000711 AC: 60AN: 84422Hom.: 1 AF XY: 0.000584 AC XY: 28AN XY: 47936
GnomAD4 exome AF: 0.000599 AC: 794AN: 1324944Hom.: 9 Cov.: 30 AF XY: 0.000529 AC XY: 345AN XY: 652384
GnomAD4 genome ? AF: 0.00842 AC: 1277AN: 151666Hom.: 24 Cov.: 31 AF XY: 0.00815 AC XY: 604AN XY: 74112
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 01, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 22, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 27, 2013 | - - |
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at