rs149203149
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001843.4(CNTN1):āc.54T>Cā(p.Cys18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000477 in 1,598,100 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00037 ( 2 hom., cov: 32)
Exomes š: 0.00049 ( 8 hom. )
Consequence
CNTN1
NM_001843.4 synonymous
NM_001843.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.355
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 12-40908486-T-C is Benign according to our data. Variant chr12-40908486-T-C is described in ClinVar as [Benign]. Clinvar id is 469424.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.355 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000368 (56/152320) while in subpopulation SAS AF= 0.00456 (22/4828). AF 95% confidence interval is 0.00308. There are 2 homozygotes in gnomad4. There are 35 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.54T>C | p.Cys18= | synonymous_variant | 2/24 | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.54T>C | p.Cys18= | synonymous_variant | 2/24 | 1 | NM_001843.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000368 AC: 56AN: 152202Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000923 AC: 231AN: 250188Hom.: 2 AF XY: 0.00132 AC XY: 178AN XY: 135242
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GnomAD4 exome AF: 0.000488 AC: 706AN: 1445780Hom.: 8 Cov.: 27 AF XY: 0.000671 AC XY: 483AN XY: 720170
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GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152320Hom.: 2 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Compton-North congenital myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
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Name
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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