rs12367345
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001843.4(CNTN1):c.2711-17A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,492,160 control chromosomes in the GnomAD database, including 16,623 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.12 ( 1290 hom., cov: 32)
Exomes 𝑓: 0.15 ( 15333 hom. )
Consequence
CNTN1
NM_001843.4 splice_polypyrimidine_tract, intron
NM_001843.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.547
Genes affected
CNTN1 (HGNC:2171): (contactin 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 12-41027840-A-G is Benign according to our data. Variant chr12-41027840-A-G is described in ClinVar as [Benign]. Clinvar id is 258196.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.2711-17A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.2711-17A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001843.4 | P3 | |||
CNTN1 | ENST00000347616.5 | c.2711-17A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | P3 | ||||
CNTN1 | ENST00000348761.2 | c.2678-17A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
CNTN1 | ENST00000550305.1 | n.670-17A>G | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.120 AC: 18308AN: 152016Hom.: 1289 Cov.: 32
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GnomAD3 exomes AF: 0.128 AC: 32092AN: 250542Hom.: 2301 AF XY: 0.129 AC XY: 17464AN XY: 135402
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GnomAD4 exome AF: 0.147 AC: 196985AN: 1340026Hom.: 15333 Cov.: 22 AF XY: 0.145 AC XY: 97783AN XY: 673624
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GnomAD4 genome ? AF: 0.120 AC: 18308AN: 152134Hom.: 1290 Cov.: 32 AF XY: 0.120 AC XY: 8957AN XY: 74360
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 08, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Compton-North congenital myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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