chr1-205064390-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_005076.5(CNTN2):āc.1309C>Gā(p.Leu437Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0166 in 1,612,364 control chromosomes in the GnomAD database, including 530 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_005076.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN2 | NM_005076.5 | c.1309C>G | p.Leu437Val | missense_variant | 11/23 | ENST00000331830.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN2 | ENST00000331830.7 | c.1309C>G | p.Leu437Val | missense_variant | 11/23 | 1 | NM_005076.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0349 AC: 5305AN: 152154Hom.: 172 Cov.: 32
GnomAD3 exomes AF: 0.0179 AC: 4508AN: 251172Hom.: 120 AF XY: 0.0168 AC XY: 2276AN XY: 135760
GnomAD4 exome AF: 0.0147 AC: 21517AN: 1460092Hom.: 357 Cov.: 32 AF XY: 0.0146 AC XY: 10571AN XY: 725954
GnomAD4 genome AF: 0.0349 AC: 5320AN: 152272Hom.: 173 Cov.: 32 AF XY: 0.0338 AC XY: 2517AN XY: 74450
ClinVar
Submissions by phenotype
Epilepsy, familial adult myoclonic, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at