rs71148543
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_000743.5(CHRNA3):c.*162_*163del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,120,818 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00025 ( 1 hom., cov: 0)
Exomes 𝑓: 0.0013 ( 2 hom. )
Consequence
CHRNA3
NM_000743.5 3_prime_UTR
NM_000743.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.830
Genes affected
CHRNA3 (HGNC:1957): (cholinergic receptor nicotinic alpha 3 subunit) This locus encodes a member of the nicotinic acetylcholine receptor family of proteins. Members of this family of proteins form pentameric complexes comprised of both alpha and beta subunits. This locus encodes an alpha-type subunit, as it contains characteristic adjacent cysteine residues. The encoded protein is a ligand-gated ion channel that likely plays a role in neurotransmission. Polymorphisms in this gene have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000253 (38/149990) while in subpopulation SAS AF= 0.00568 (27/4752). AF 95% confidence interval is 0.00401. There are 1 homozygotes in gnomad4. There are 26 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA3 | NM_000743.5 | c.*162_*163del | 3_prime_UTR_variant | 6/6 | ENST00000326828.6 | ||
CHRNA3 | XM_006720382.4 | c.*162_*163del | 3_prime_UTR_variant | 6/6 | |||
CHRNA3 | NM_001166694.2 | c.1390-3251_1390-3250del | intron_variant | ||||
CHRNA3 | NR_046313.2 | n.1784+98_1784+99del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA3 | ENST00000326828.6 | c.*162_*163del | 3_prime_UTR_variant | 6/6 | 1 | NM_000743.5 | P1 | ||
CHRNA3 | ENST00000348639.7 | c.1390-3251_1390-3250del | intron_variant | 1 | |||||
CHRNA3 | ENST00000559002.5 | n.193+98_193+99del | intron_variant, non_coding_transcript_variant | 1 | |||||
CHRNA3 | ENST00000559658.5 | c.*64+98_*64+99del | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000260 AC: 39AN: 149884Hom.: 1 Cov.: 0
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GnomAD4 exome AF: 0.00135 AC: 1308AN: 970828Hom.: 2 AF XY: 0.00147 AC XY: 677AN XY: 462086
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GnomAD4 genome ? AF: 0.000253 AC: 38AN: 149990Hom.: 1 Cov.: 0 AF XY: 0.000355 AC XY: 26AN XY: 73200
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ClinVar
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at