chr15-78601529-G-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000743.5(CHRNA3):āc.1113C>Gā(p.Pro371=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,048 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 (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 31)
Exomes š: 0.0000068 ( 0 hom. )
Consequence
CHRNA3
NM_000743.5 synonymous
NM_000743.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.284
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 15-78601529-G-C is Benign according to our data. Variant chr15-78601529-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 744231.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.284 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA3 | NM_000743.5 | c.1113C>G | p.Pro371= | synonymous_variant | 5/6 | ENST00000326828.6 | |
CHRNA3 | NM_001166694.2 | c.1113C>G | p.Pro371= | synonymous_variant | 5/6 | ||
CHRNA3 | XM_006720382.4 | c.912C>G | p.Pro304= | synonymous_variant | 5/6 | ||
CHRNA3 | NR_046313.2 | n.1315C>G | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA3 | ENST00000326828.6 | c.1113C>G | p.Pro371= | synonymous_variant | 5/6 | 1 | NM_000743.5 | P1 | |
CHRNA3 | ENST00000348639.7 | c.1113C>G | p.Pro371= | synonymous_variant | 5/6 | 1 | |||
CHRNA3 | ENST00000559658.5 | c.1113C>G | p.Pro371= | synonymous_variant, NMD_transcript_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251246Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135790
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727248
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74328
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 09, 2023 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at