chr3-1278457-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 8P and 8B. PVS1BP6_Very_Strong
The NM_001289080.2(CNTN6):c.403C>T(p.Arg135Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000293 in 1,612,152 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001289080.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN6 | NM_001289080.2 | c.403C>T | p.Arg135Ter | stop_gained | 5/23 | ENST00000446702.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN6 | ENST00000446702.7 | c.403C>T | p.Arg135Ter | stop_gained | 5/23 | 1 | NM_001289080.2 | P1 | |
CNTN6 | ENST00000350110.2 | c.403C>T | p.Arg135Ter | stop_gained | 5/23 | 1 | P1 | ||
CNTN6 | ENST00000394261.2 | c.*381C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 1 | ||||
CNTN6 | ENST00000397479.6 | c.*541C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 151972Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000522 AC: 131AN: 251096Hom.: 1 AF XY: 0.000508 AC XY: 69AN XY: 135720
GnomAD4 exome AF: 0.000294 AC: 430AN: 1460180Hom.: 2 Cov.: 30 AF XY: 0.000285 AC XY: 207AN XY: 726328
GnomAD4 genome ? AF: 0.000283 AC: 43AN: 151972Hom.: 0 Cov.: 33 AF XY: 0.000270 AC XY: 20AN XY: 74204
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | CNTN6: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at