rs141733086
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_000079.4(CHRNA1):c.948C>A(p.Ile316=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000152 in 1,614,138 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 0 hom. )
Consequence
CHRNA1
NM_000079.4 synonymous
NM_000079.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.84
Genes affected
CHRNA1 (HGNC:1955): (cholinergic receptor nicotinic alpha 1 subunit) The muscle acetylcholine receptor consiststs of 5 subunits of 4 different types: 2 alpha subunits and 1 each of the beta, gamma, and delta subunits. This gene encodes an alpha subunit that plays a role in acetlycholine binding/channel gating. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 2-174750000-G-T is Benign according to our data. Variant chr2-174750000-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 198389.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA1 | NM_000079.4 | c.948C>A | p.Ile316= | synonymous_variant | 7/9 | ENST00000348749.9 | |
CHRNA1 | NM_001039523.3 | c.1023C>A | p.Ile341= | synonymous_variant | 8/10 | ||
CHRNA1 | XM_017003256.2 | c.1044C>A | p.Ile348= | synonymous_variant | 7/9 | ||
CHRNA1 | XM_017003257.2 | c.969C>A | p.Ile323= | synonymous_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA1 | ENST00000348749.9 | c.948C>A | p.Ile316= | synonymous_variant | 7/9 | 1 | NM_000079.4 | P1 | |
ENST00000442996.1 | n.321+20176G>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152138Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000159 AC: 40AN: 251256Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135786
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GnomAD4 exome AF: 0.000156 AC: 228AN: 1461882Hom.: 0 Cov.: 34 AF XY: 0.000135 AC XY: 98AN XY: 727244
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GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74464
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 15, 2014 | - - |
Lethal multiple pterygium syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
CHRNA1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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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