chr3-1278437-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001289080.2(CNTN6):c.383C>T(p.Thr128Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00021 in 1,608,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001289080.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN6 | NM_001289080.2 | c.383C>T | p.Thr128Ile | missense_variant | 5/23 | ENST00000446702.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN6 | ENST00000446702.7 | c.383C>T | p.Thr128Ile | missense_variant | 5/23 | 1 | NM_001289080.2 | P1 | |
CNTN6 | ENST00000350110.2 | c.383C>T | p.Thr128Ile | missense_variant | 5/23 | 1 | P1 | ||
CNTN6 | ENST00000394261.2 | c.*361C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 1 | ||||
CNTN6 | ENST00000397479.6 | c.*521C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00122 AC: 185AN: 152058Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000289 AC: 72AN: 249480Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 134772
GnomAD4 exome AF: 0.000105 AC: 153AN: 1455984Hom.: 0 Cov.: 30 AF XY: 0.0000857 AC XY: 62AN XY: 723692
GnomAD4 genome AF: 0.00122 AC: 185AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.00112 AC XY: 83AN XY: 74398
ClinVar
Submissions by phenotype
CNTN6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 04, 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at