3-1220802-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001289080.2(CNTN6):c.171G>A(p.Ser57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000487 in 1,601,572 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
CNTN6
NM_001289080.2 synonymous
NM_001289080.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.502
Genes affected
CNTN6 (HGNC:2176): (contactin 6) 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 3-1220802-G-A is Benign according to our data. Variant chr3-1220802-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3048542.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.502 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN6 | NM_001289080.2 | c.171G>A | p.Ser57= | synonymous_variant | 3/23 | ENST00000446702.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN6 | ENST00000446702.7 | c.171G>A | p.Ser57= | synonymous_variant | 3/23 | 1 | NM_001289080.2 | P1 | |
CNTN6 | ENST00000350110.2 | c.171G>A | p.Ser57= | synonymous_variant | 3/23 | 1 | P1 | ||
CNTN6 | ENST00000394261.2 | c.*149G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/8 | 1 | ||||
CNTN6 | ENST00000397479.6 | c.*309G>A | 3_prime_UTR_variant, NMD_transcript_variant | 2/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 151942Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000494 AC: 12AN: 242688Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131208
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GnomAD4 exome AF: 0.0000386 AC: 56AN: 1449630Hom.: 0 Cov.: 31 AF XY: 0.0000333 AC XY: 24AN XY: 721002
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CNTN6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 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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Benign
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at