rs371816961
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 3P and 9B. PM2PP2BP4_StrongBP6BS1
The NM_005076.5(CNTN2):c.1075C>A(p.Arg359Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000305 in 1,612,954 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R359H) has been classified as Uncertain significance.
Frequency
Consequence
NM_005076.5 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTN2 | NM_005076.5 | c.1075C>A | p.Arg359Ser | missense_variant | 9/23 | ENST00000331830.7 | NP_005067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTN2 | ENST00000331830.7 | c.1075C>A | p.Arg359Ser | missense_variant | 9/23 | 1 | NM_005076.5 | ENSP00000330633.4 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000730 AC: 181AN: 247836Hom.: 0 AF XY: 0.00103 AC XY: 138AN XY: 134580
GnomAD4 exome AF: 0.000318 AC: 465AN: 1460580Hom.: 1 Cov.: 30 AF XY: 0.000469 AC XY: 341AN XY: 726600
GnomAD4 genome AF: 0.000177 AC: 27AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74512
ClinVar
Submissions by phenotype
Epilepsy, familial adult myoclonic, 5 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Apr 06, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at