3-129171507-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_003418.5(CNBP):c.156C>A(p.Asp52Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 152,142 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. D52D) has been classified as Benign.
Frequency
Consequence
NM_003418.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNBP | NM_003418.5 | c.156C>A | p.Asp52Glu | missense_variant | 3/5 | ENST00000422453.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNBP | ENST00000422453.7 | c.156C>A | p.Asp52Glu | missense_variant | 3/5 | 1 | NM_003418.5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251466Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135908
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000105 AC: 154AN: 1461872Hom.: 0 Cov.: 57 AF XY: 0.0000990 AC XY: 72AN XY: 727244
GnomAD4 genome AF: 0.000138 AC: 21AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74330
ClinVar
Submissions by phenotype
Myotonic dystrophy type 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 21, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at