chr1-205058028-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000331830.7(CNTN2):c.178G>A(p.Ala60Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00209 in 1,613,400 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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. A60V) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000331830.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTN2 | NM_005076.5 | c.178G>A | p.Ala60Thr | missense_variant | 3/23 | ENST00000331830.7 | NP_005067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTN2 | ENST00000331830.7 | c.178G>A | p.Ala60Thr | missense_variant | 3/23 | 1 | NM_005076.5 | ENSP00000330633 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1766AN: 152160Hom.: 34 Cov.: 32
GnomAD3 exomes AF: 0.00294 AC: 737AN: 250328Hom.: 15 AF XY: 0.00219 AC XY: 296AN XY: 135446
GnomAD4 exome AF: 0.00109 AC: 1590AN: 1461122Hom.: 33 Cov.: 32 AF XY: 0.000944 AC XY: 686AN XY: 726842
GnomAD4 genome AF: 0.0117 AC: 1775AN: 152278Hom.: 35 Cov.: 32 AF XY: 0.0113 AC XY: 841AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Epilepsy, familial adult myoclonic, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at