3-1278503-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001289080.2(CNTN6):āc.449T>Cā(p.Phe150Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00346 in 1,610,972 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001289080.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN6 | NM_001289080.2 | c.449T>C | p.Phe150Ser | missense_variant | 5/23 | ENST00000446702.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN6 | ENST00000446702.7 | c.449T>C | p.Phe150Ser | missense_variant | 5/23 | 1 | NM_001289080.2 | P1 | |
CNTN6 | ENST00000350110.2 | c.449T>C | p.Phe150Ser | missense_variant | 5/23 | 1 | P1 | ||
CNTN6 | ENST00000394261.2 | c.*427T>C | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 1 | ||||
CNTN6 | ENST00000397479.6 | c.*587T>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2341AN: 152052Hom.: 64 Cov.: 33
GnomAD3 exomes AF: 0.00527 AC: 1322AN: 250768Hom.: 23 AF XY: 0.00400 AC XY: 542AN XY: 135560
GnomAD4 exome AF: 0.00221 AC: 3220AN: 1458802Hom.: 67 Cov.: 29 AF XY: 0.00201 AC XY: 1456AN XY: 725600
GnomAD4 genome AF: 0.0154 AC: 2346AN: 152170Hom.: 64 Cov.: 33 AF XY: 0.0149 AC XY: 1108AN XY: 74400
ClinVar
Submissions by phenotype
CNTN6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 13, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at