12-40939386-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP6BS1
The NM_001843.4(CNTN1):āc.1280C>Gā(p.Ala427Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,613,762 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). Synonymous variant affecting the same amino acid position (i.e. A427A) has been classified as Likely benign.
Frequency
Consequence
NM_001843.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.1280C>G | p.Ala427Gly | missense_variant | 12/24 | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.1280C>G | p.Ala427Gly | missense_variant | 12/24 | 1 | NM_001843.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 250976Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135612
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461648Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727112
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74298
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 18, 2024 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Compton-North congenital myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at