chr11-100061213-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_014361.4(CNTN5):c.982C>G(p.Pro328Ala) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000932 in 1,605,812 control chromosomes in the GnomAD database, including 5 homozygotes. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P328S) has been classified as Uncertain significance.
Frequency
Consequence
NM_014361.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN5 | NM_014361.4 | c.982C>G | p.Pro328Ala | missense_variant, splice_region_variant | 10/25 | ENST00000524871.6 | |
LOC105369456 | XR_947948.3 | n.208-5683G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN5 | ENST00000524871.6 | c.982C>G | p.Pro328Ala | missense_variant, splice_region_variant | 10/25 | 1 | NM_014361.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000756 AC: 115AN: 152060Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000851 AC: 211AN: 247854Hom.: 1 AF XY: 0.000930 AC XY: 125AN XY: 134438
GnomAD4 exome AF: 0.000950 AC: 1381AN: 1453634Hom.: 3 Cov.: 31 AF XY: 0.000959 AC XY: 692AN XY: 721836
GnomAD4 genome ? AF: 0.000756 AC: 115AN: 152178Hom.: 2 Cov.: 33 AF XY: 0.000645 AC XY: 48AN XY: 74390
ClinVar
Submissions by phenotype
CNTN5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2022 | 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