rs892413
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004198.3(CHRNA6):c.220-122G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 732,570 control chromosomes in the GnomAD database, including 30,168 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 13355 hom., cov: 31)
Exomes 𝑓: 0.22 ( 16813 hom. )
Consequence
CHRNA6
NM_004198.3 intron
NM_004198.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.17
Genes affected
CHRNA6 (HGNC:15963): (cholinergic receptor nicotinic alpha 6 subunit) This gene encodes an alpha subunit of neuronal nicotinic acetylcholine receptors. These receptors consist of five subunits and function as ion channels involved in neurotransmission. The encoded protein is a subunit of neuronal nicotinic acetylcholine receptors that mediate dopaminergic neurotransmission and are activated by acetylcholine and exogenous nicotine. Alternatively spliced transcript variants have been observed for this gene. Single nucleotide polymorphisms in this gene have been associated with both nicotine and alcohol dependence. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA6 | NM_004198.3 | c.220-122G>T | intron_variant | ENST00000276410.7 | |||
CHRNA6 | NM_001199279.1 | c.220-2198G>T | intron_variant | ||||
CHRNA6 | XM_047422396.1 | c.220-122G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA6 | ENST00000276410.7 | c.220-122G>T | intron_variant | 1 | NM_004198.3 | P1 | |||
CHRNA6 | ENST00000533810.5 | c.-18-122G>T | intron_variant | 4 | |||||
CHRNA6 | ENST00000534622.5 | c.220-2198G>T | intron_variant | 2 | |||||
CHRNA6 | ENST00000530869.1 | n.466-122G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.351 AC: 53257AN: 151908Hom.: 13314 Cov.: 31
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GnomAD4 exome AF: 0.222 AC: 128944AN: 580544Hom.: 16813 Cov.: 7 AF XY: 0.218 AC XY: 68043AN XY: 311684
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GnomAD4 genome ? AF: 0.351 AC: 53356AN: 152026Hom.: 13355 Cov.: 31 AF XY: 0.345 AC XY: 25627AN XY: 74304
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at