12-40908549-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001843.4(CNTN1):c.61+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,257,056 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 18 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 17 hom. )
Consequence
CNTN1
NM_001843.4 intron
NM_001843.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.335
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 12-40908549-G-A is Benign according to our data. Variant chr12-40908549-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1198402.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00893 (1359/152252) while in subpopulation AFR AF= 0.0308 (1281/41562). AF 95% confidence interval is 0.0294. There are 18 homozygotes in gnomad4. There are 651 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.61+56G>A | intron_variant | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.61+56G>A | intron_variant | 1 | NM_001843.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00893 AC: 1358AN: 152134Hom.: 18 Cov.: 32
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GnomAD4 exome AF: 0.000946 AC: 1045AN: 1104804Hom.: 17 AF XY: 0.000795 AC XY: 448AN XY: 563436
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GnomAD4 genome ? AF: 0.00893 AC: 1359AN: 152252Hom.: 18 Cov.: 32 AF XY: 0.00874 AC XY: 651AN XY: 74446
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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 | GeneDx | Jul 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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