3-3042759-A-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_175607.3(CNTN4):c.2512-218A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 605,162 control chromosomes in the GnomAD database, including 5,658 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2888 hom., cov: 33)
Exomes 𝑓: 0.096 ( 2770 hom. )
Consequence
CNTN4
NM_175607.3 intron
NM_175607.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.683
Genes affected
CNTN4 (HGNC:2174): (contactin 4) This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 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=-0.81).
BP6
Variant 3-3042759-A-T is Benign according to our data. Variant chr3-3042759-A-T is described in ClinVar as [Benign]. Clinvar id is 1287127.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTN4 | NM_175607.3 | c.2512-218A>T | intron_variant | ENST00000418658.6 | NP_783200.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTN4 | ENST00000418658.6 | c.2512-218A>T | intron_variant | 5 | NM_175607.3 | ENSP00000396010.1 |
Frequencies
GnomAD3 genomes AF: 0.159 AC: 24143AN: 152024Hom.: 2871 Cov.: 33
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GnomAD4 exome AF: 0.0961 AC: 43546AN: 453020Hom.: 2770 AF XY: 0.0947 AC XY: 22820AN XY: 241028
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GnomAD4 genome AF: 0.159 AC: 24193AN: 152142Hom.: 2888 Cov.: 33 AF XY: 0.153 AC XY: 11414AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 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