rs34326474
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001843.4(CNTN1):c.2324G>A(p.Ser775Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00171 in 1,614,034 control chromosomes in the GnomAD database, including 48 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S775I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001843.4 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 |
---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.2324G>A | p.Ser775Asn | missense_variant | 19/24 | ENST00000551295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.2324G>A | p.Ser775Asn | missense_variant | 19/24 | 1 | NM_001843.4 | P3 | |
CNTN1 | ENST00000347616.5 | c.2324G>A | p.Ser775Asn | missense_variant | 18/23 | 1 | P3 | ||
CNTN1 | ENST00000348761.2 | c.2291G>A | p.Ser764Asn | missense_variant | 17/22 | 1 | A1 | ||
CNTN1 | ENST00000550305.1 | n.283G>A | non_coding_transcript_exon_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00909 AC: 1383AN: 152068Hom.: 23 Cov.: 32
GnomAD3 exomes AF: 0.00247 AC: 620AN: 251398Hom.: 9 AF XY: 0.00178 AC XY: 242AN XY: 135864
GnomAD4 exome AF: 0.000938 AC: 1371AN: 1461848Hom.: 25 Cov.: 32 AF XY: 0.000815 AC XY: 593AN XY: 727224
GnomAD4 genome AF: 0.00911 AC: 1387AN: 152186Hom.: 23 Cov.: 32 AF XY: 0.00844 AC XY: 628AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 29, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 23, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Compton-North congenital myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at